First of all, I'm not sure if this first issue is a bug or not, but everyone's disposition towards me is always extremely low, like 10 or less. This is causing some problems when a mod I use spawns a creature follower, who then decides to go on a killing spree because of the low disposition from everyone.
The second issue I've recently noticed, is that in certain cells with Ascended Sleepers, once you kill them there's a chance the cells lighting becomes fubared to the point you can't see anything, torches don't light anything up, and the local map ceases to work (and in fact gets wiped somehow). This kept happening with Dagoth Goral.
The last issue I've "fixed" myself, but felt like it needs to be brought to attention anyway. Somehow there's a script somewhere that goes rogue and messes with enemy AI. Enemies will be stuck unable to move (unless they do lunge attacks), and even in some cases not even recognizing me as a thread. I "solved" the issue by making a copy of Morroblivion with all scripts removed, then loading + saving a new game, then restoring the original Morroblivion plugin. Verified that it was coming from Morroblivion as I deactivated all mods, tested on new and old saves, then did the same with Morroblivion deactivated, etc. Very dirty and digusting way of going around the issue but I couldn't figure out a way of correcting it and don't mind having to use the console for any quests that might have broke.