All the instances listed were tested over a solid week of solo grind (unless stated), using Horde character's. If you become stuck but this list says it works then check the dungeon/raid guides or check the comments for tips on wowhead by clicking the instance names below.
Most issues aren't actually issues and are either waiting for script timings to play out, an interactive object to be used or you killed the boss too quick.
A tip: Try not to one shot the bosses, let them hurt you for a bit.
Raids were tested on the hardest mode available, while Dungeons on Heroic and Normal when forced, check side notes if issues persist in a specific version.
As Shadowkeep is the current realms expansion any issues in those instances get fixed pretty quick so they won't be listed.
A seperate list for Legacy Dungeon Mythics is in production.
In no means is this a "fix it now" list for Devs, this is for the community, to save time when farming content.
If anything below is different for you, if something works or doesnt, leave a comment or shoot me an ingame message. Open: Is Instance available to enter? Loot: Does Instance have the correct loot table? Script: Is the Instance scripted enough to complete?
Press F3 and type the name of a specific Instance for easier navigation.

Edit: Missed instances are at the bottom.   Instance Open Loot Script   Issue / Notes  Blackfathom Deeps YES YES NO  Aku'mais chamber doors won't open after killing Twilight Lord Bathiel and interacting with Fire of Aku'mai braziers - Unable to finish the dungeon.   Blackrock Depths YES YES NO  All encounters inside the Grim Guzzler are non interactive, exit is locked until they are completed - Unable to finish the dungeon.  The Deadmines YES YES NO  Gunpowder to use on Defias Cannon for opening the final area is an attackable object, not usable - Unable to finish the dungeon.  Dire Maul YES YES YES  Gordok Ogre Suit doesnt work.  Gnomeregan YES YES YES  Grubbis can't spawn as Blastmaster Emi Shortfuse's script doesnt exist, Pressing the 'PUSH ME' button doesn't summon Endgineer Omegaplugg.  Lower Blackrock Spire YES YES YES  Rotating bridge geometry is aligned incorrectly, appears closed but can be walked through just fine.  Maraudon YES YES YES  Working as Intended.  Razorfen Downs YES NO YES  Aarux, Mordresh Fire Eye, Death Speaker Blackthorn, Amnennar the Coldbringer, = No Loot  Razorfen Kraul YES YES YES  Working as Intended.  Scarlet Halls YES YES YES  Bucket of Meaty Dog Food stunlocks the player, requires Unstuck to fix. Obedient Hound not scripted, Scarlet Guardian's are unkillable, unscripted.  Scarlet Monastery YES YES NO  High inquisitor Whitemane is unattackable - Unable to finish the dungeon.  Scholomance YES YES YES  Working as Intended.  Shadowfang Keep YES YES YES  Working as Intended.  Stratholme YES YES YES  Working as Intended.  The Stockade YES YES YES  Working as Intended.  The Temple of Atal'Hakkar YES NO YES  Avatar of Hakkar, Weaver, Dreamscythe, Morphaz, Hazzas = No Loot, Egg of Hakkar is dropping it should no longer drop.  Uldaman YES YES NO  Archaedas isn't scripted after activating his trigger to start the encounter - Unable to finish the dungeon.  Wailing Caverns YES YES YES  Working as Intended.  Zul'Farrak YES YES YES  Working as Intended.  Molten Core YES YES YES  Majordomo Executus is already dead, his loot cache is available nearby.  Onyxia's Lair YES YES YES  Working as Intended.  Blackwing Lair YES YES YES  Working as Intended.  Ruins of Ahn'Qiraj YES YES YES  Working as Intended.  Temple of Ahn'Qiraj YES YES YES  Working as Intended.  Instance Open Loot Script  Issue / Notes  Auchenai Crypts YES YES YES  Working as Intended.  Hellfire Ramparts YES YES YES  Working as Intended.  Magisters' Terrace YES YES YES  Scrying Orb Camera isn't scripted properly and it can stack summon Kalecgos an infinite number of times.  Mana-Tombs YES YES YES  Working as Intended.  Old Hillsbrad Foothills YES YES NO  After escorting Thrall to Taretha, Epoch Hunter doesnt spawn - Unable to finish the dungeon.  Sethekk Halls YES YES YES  Working as Intended.  Shadow Labyrinth YES YES YES  Working as Intended.  The Arcatraz YES YES YES  Working as Intended.  The Black Morass YES NO NO  Chrono Lord Deja, Temporus = No Loot, Aeonus doesn't spawn - Unable to finish the dungeon.  The Botanica YES YES YES  Working as Intended.  The Mechanar YES YES YES  Working as Intended.  The Shattered Halls YES YES YES  Working as Intended.  The Slave Pens YES YES YES  Working as Intended.  The Steamvault YES YES YES  Working as Intended.  The Underbog YES YES YES  Working as Intended.  Karazhan YES YES NO  Nightbane is already free and wil head straight for the player through geometry. Opera Hall stop's progressing and player will become stuck, teleporting or Unstucking will lock you out of the instance - Unable to finish the raid.  Gruul's Lair YES YES YES  Working as Intended.  Magtheridon's Lair YES YES YES  Working as Intended.  Serpentshrine Cavern YES YES YES  The Lurker Below can't be encountered as fishing in central area isn't allowed.  The Eye YES YES YES  Kael'thas Sunstrider takes his sweet time between phases, just be patient.  The Battle for Mount Hyjal YES YES YES  Working as Intended.  Black Temple YES YES NO  Shade of Akama encounter won't start, Illidan Stormrage stops working when dialogue with Maiev ends - Unable to finish the raid.  Sunwell Plateau YES YES YES  Brutallus is immune to attacks, Workaround: restarting encounter with suicide fixes this.  Instance Open Loot Script  Issue / Notes  Ahn'kahet: The Old Kingdom YES NO YES  Prince Taldaram, Amanitar  = No Loot  Azjol-Nerub YES YES YES  Working as Intended.  Drak'Tharon Keep YES YES YES  Scourge Reanimator's will aggro but are unattackable, Risen Drakkari Bat Rider's are non interactive yet aggro and attack the player.  Gundrak YES YES YES  Working as Intended.  Halls of Lightning YES YES YES  Working as Intended.  Halls of Reflection YES YES YES  During escape phase make sure to kill all the minions that get summoned to move through each phase, DO NOT run to the end until Arthas starts running.  Halls of Stone YES YES NO  Tribunal of Ages not scripted properly, one shots the player and then dungeon becomes soft locked - Unable to finish the dungeon.  Pit of Saron YES YES YES  Working as Intended.  The Culling of Stratholme YES YES YES  Working as Intended.  The Forge of Souls YES YES YES  Working as Intended.  The Nexus YES YES NO  Keristrasza when awakened, becomes unattackable but can still attack the player - Unable to finish the dungeon.  The Oculus YES YES NO  Ley-Guardian Eregos does not spawn - Unable to finish the dungeon.  The Violet Hold YES ? NO  Lieutenant Sinclari can't be interacted with to start the encounter - Unable to finish the dungeon.  Trial of the Champion YES YES NO  After defeating Argent Confessor Paletress No chest spawns - Unable to finish the dungeon.  Utgarde Keep YES YES YES  Working as Intended.  Utgarde Pinnacle YES YES YES  Svala Sorrowgrave isn't attackable and loses intelligence after her conversation with the Lich King.  Vault of Archavon YES YES YES  Working as Intended.  Naxxramas YES YES NO  Kel'Thuzad isn't damagable during second phase of fight when he should be (tested with multiple players) - Unable to finish the raid.  The Obsidian Sanctum YES YES YES  Working as Intended.  The Eye of Eternity YES ? NO  Malygos is not attackable - Unable to finish the raid.  Ulduar YES YES NO  Thorim has script failure, unable to challenge him, General Vezax doesn't spawn, Mimiron's railway doesn't work - Unable to finish the raid.  Trial of the Crusader YES ? NO  Barrett Ramsey can't be interacted with to start the encounter - Unable to finish the raid.  Icecrown Citadel YES NO NO  Too many issues to list, the worst version of ICC i've played on Firestorm realms, can't activate final elevator - Unable to finish the raid.  The Ruby Sanctum YES YES YES  Working as Intended.  Instance Open Loot Script  Issue / Notes  Blackrock Caverns YES YES YES  Working as Intended.  End Time YES YES YES  Working as Intended.  Grim Batol YES YES YES  Working as Intended.  Halls of Origination YES YES YES  Working as Intended.  Hour of Twilight YES YES YES  Working as Intended.  Lost City of the Tol'Vir YES YES YES  Working as Intended.  The Stonecore YES YES YES  Working as Intended.  The Vortex Pinnacle YES YES YES  Working as Intended.  Throne of the Tides YES YES NO  Commander Ulthok doesn't spawn, Tentacles blocking the way to Ozumat and Mindbender Ghur'sha cannot be removed - Unable to finish the dungeon.  Well of Eternity YES ? NO  Completely empty of NPC's and Enemies, first fire wall cannot be disabled due to this - Unable to finish the dungeon.  Zul'Aman YES YES YES  Working as Intended.  Zul'Gurub YES YES NO  Cache of Madness event won't activate. Jin'do the Godbreaker fails to leave stage 2 - Unable to finish the dungeon.  Baradin Hold YES YES YES  Working as Intended.  Blackwing Descent YES YES YES  Working as Intended.  The Bastion of Twilight YES YES YES  Working as Intended.  Throne of the Four Winds YES YES YES  Working as Intended.  Firelands YES YES YES  Killing Ragnaros too quick can cause his corpse/hammer to become un-lootable.  Dragon Soul YES YES NO  Ultraxion is invisible, non targetable/damagable she continues to hit you with a melee, perma aggro - Unable to finish the raid.  Instance Open Loot Script  Issue / Notes  Gate of the Setting Sun YES NO YES  Raigonn has incorrect loot pool.  Mogu'shan Palace YES NO YES  Gekkan's pile of loot gives no loot, vault boxes can't be looted either.  Shado-Pan Monastery YES ? NO  Gu Cloudstrike starts the fight stuck in phase 2 and the Azure Serpent isn't targetable - Unable to finish the dungeon.  Siege of Niuzao Temple YES YES NO  After defeating General Pa'valak an endless stream of Sik'thik Soldier's spawn, invisible barrier blocking way to final boss - Unable to finish the dungeon.  Stormstout Brewery YES YES YES  Working as Intended.  Temple of the Jade Serpent YES YES YES  Working as Intended.  Mogu'shan Vaults YES YES YES  Working as Intended.  Heart of Fear YES YES YES  Working as Intended.  Terrace of Endless Spring YES YES YES  Working as Intended.  Throne of Thunder YES YES NO  Megaera fight doesnt exist, door to next encounter locked - Unable to finish the raid.  Siege of Orgrimmar YES NO NO  Immerseus  = No Loot, Dragonmaw Cannoneer will attach to cannon's making cannon and themself immune to damage, softlocking the instance in Dranosh'ar Landing - Unable to finish the raid.  Instance Open Loot Script  Issue / Notes  Auchindoun YES YES NO  Barrier blocking access to Teron'gor won't open - Unable to finish the dungeon.  Bloodmaul Slag Mines YES ? NO  Barrier blocking entry into dungeon won't open - Unable to finish the dungeon.  Grimrail Depot YES NO YES  Skylord Tovra = No Loot  Iron Docks YES NO YES  Grimrail Enforcers = No Loot  Shadowmoon Burial Grounds NO ? ?  Unable to enter the dungeon.  Skyreach YES YES NO  Rukhran isn't targetable - Unable to finish the dungeon.  The Everbloom YES YES NO  Witherbark gets stuck in a Brittle Bark recast and can't be attacked - Unable to finish the dungeon.  Upper Blackrock Spire YES ? NO  Barrier blocking entry into dungeon won't open - Unable to finish the dungeon.  Highmaul YES ? NO  After killing first wave of ads no further progress happens in The Coliseum - Unable to finish the raid.  Blackrock Foundry YES YES YES  Operator Thogar cant be activated thus Iron Maidens also cant be completed, During Blackhand if he dies mid floor you lose chance at loot.  Hellfire Citadel YES YES YES  Working as Intended.  Instance Open Loot Done  Issue / Notes  Assault on Violet Hold YES NO YES  Can't loot corpses as thay are set to auto fade, Millificent's Discarded Lockbox cannot be looted.  Black Rook Hold YES YES YES  Lord Kur'talos Ravencrest may be immune in first phase, this will fix itself in second phase.  Cathedral of Eternal Night YES YES YES  Working as Intended.  Court of Stars YES YES YES  Working as Intended.  Darkheart Thicket YES YES YES  Working as Intended.  Eye of Azshara YES YES YES  Working as Intended.  Halls of Valor YES YES NO  Odyn does'nt begin attack phase after defeating his four champions - Unable to finish the dungeon.  Maw of Souls YES YES YES  Working as Intended.  Neltharion's Lair YES YES YES  Rider's are unkillable after killing Emberhusk Dominator's and are perma aggro'd.  Return to Karazhan YES NO    Moroes = No Loot = No Key to Enter Upper Karazhan  Seat of the Triumvirate NO ? ?  Unable to enter the dungeon.  The Arcway NO ? ?  Unable to enter the dungeon.  Vault of the Wardens YES YES YES  Bridge does'nt work after defeating Ash'golm, agility abilites/suicide can bypass it.  The Emerald Nightmare YES YES YES  Working as Intended.  Trial of Valor YES YES YES  Working as Intended.  The Nighthold YES NO YES  Gul'dan = No Loot  Tomb of Sargeras YES YES YES  Working as Intended.  Antorus, the Burning Throne YES YES NO  After killing Garothi Worldbreaker the teleporter link that appears auto sends you to the Antoran High Command where you become stuck - Unable to finish the raid.  Instance Open Loot Done  Issue / Notes  Atal'Dazar YES YES YES  Working as Intended.  Freehold YES YES YES  Working as Intended.  Kings' Rest YES YES YES  Working as Intended.  Operation: Mechagon YES YES YES  Working as Intended.  Shrine of the Storm YES YES YES  Working as Intended.  Siege of Boralus YES NO YES  Viq'goth = No Loot  Temple of the Sethraliss YES YES NO  During the Avatar of Sethraliss encouter no more Heart Guardian's spawn allowing you to heal the encounter - Unable to finish the dungeon.  The MOTHERLODE!! YES NO YES  All bosses appear to have generic trash mob loot.  The Underrot YES YES YES  Working as Intended.  Tol Dagor YES YES YES  Working as Intended.  Waycrest manor YES YES NO  Heartsbane Triad lock themselves to prevent death, corpse still attacking, unable to reset - Unable to finish the dungeon.  Uldir YES YES YES  Working as Intended.  Battle of Dazar'alor YES ? NO  Completely empty of NPC's and Enemies - Unable to finish the raid.  Crucible of Storms ? ? ?  Needs testing.  The Eternal Palace ? ? ?  Needs testing.  Ny'alotha, the Waking City ? ? ?  Needs testing.     Missed Instances:  Instance Open Loot Script  Issue / Notes  Ragefire Chasm - WoW YES YES YES  Working as Intended.  The Blood Funace -TBC YES YES YES  Working as Intended.   Thanks for checking this out, a follow and maybe a comment would be appreciated.