During the fighter's guild quest in Helnim "Hunting Twilight" TR_m2_FG_Hartise_Twilight The winged twilight is seemingly bugged in a way im not sure whats broken. It can still damage me, but if I cast a spell the spell doesnt "go off" and blocks Guuljhka as if it was a physical obstacle. Additionally any attacks done with a weapon do no damage, beyond that it seems to clip thru the creature itself. I'm not an expert on mods or anything for morrowind but did attempt to kill the creature in console sethealth 0 and that also had no effect.
In quest "Fighters Guild: For a Few Pieces of Iron" (TR_m4_FG_UshuKur3B) there is a stage, when the player can go to Shalmurat, to retrieve the stolen iron ore.
I happened to have a lot of iron ore with me, so as soon as I entered Shalmurat I received an entry, that the stolen iron has been acquired. While it's true that the player might decide to give their own ore to finish the quest, that was a confusing oversimplification.
TR_m4_TT_STF_destroy_ancient (Temple: Trial of the Saint) gets stuck, if Varos is destroyed before the start of the quest.
This is because the dialog relies on getting journal entry rather than checking Varos' dead count. And the player doesn't get this journal entry, unless the quest was started beforehands.