[Forge 1.12.2-14.23.5.2859]
[Buildcraft 7.99.24.8]

These bugs that I've found are very niche/obscure and I don't expect them to be fixed anytime soon. Perhaps a config option could be added to enable/disable machines like the Quarry from using player UUIDs as a quick fix? (if that doesn't break the mod entirely)

I've been able to reproduce bugs that that affect/are caused by the BC Quarry when these mods are present
Triumph: https://www.curseforge.com/minecraft/mc-mods/triumph/files (has mod dependencies)
Dropt: https://www.curseforge.com/minecraft/mc-mods/dropt (has mod dependency)

Triumph adds custom advancements. If a quarry breaks a block, either during construction or when mining, all uncompleted advancements become "soft-locked" for the player that owns the Quarry block. This is fixed when the Quarry is turned off and the savegame/server is reloaded. This happens because Triumph regards the Quarry's actions as the player's due to the quarry using the player's UUID. I can't tell if this is ultimately an issue with Triumph or BC since any advancement trigger set off by just the Quarry causes this soft-lock. I can't reproduce this bug with just the player or any other non-player blocks.
I can give more info on this specific issue if needed, but nothing useful appears in the .log file that I can show.

Dropt adds configurable drops to blocks that are broken. If a player breaks a block that normally drops xp, and that block's drops have been changed by Dropt, all blocks mined by a Quarry owned by that player will then drop xp. (the amount of xp that the player-broken block would originally have dropped) This is reset when a player breaks a new block that does not normally drop xp. This is a big problem with an active quarry, as the huge amounts of xp being dropped from quarry-mined blocks will freeze and crash your game/server. Installing a mod like Clumps mitigates this, but doesn't stop huge amounts of xp being dropped.