One off glitches/bugs and other strangeness (annoying)

I'm interested in any stories about annoying weirdness in the game. These are odd bugs and curious glitches that actually caused a problem, I've created another tread for ones that were either funny or useful.

Here goes:

I had a strange spell permanency issue where after fighting Zugtmoy my party were left with the visual effects of various buff spells after resting. This happens and tho aesthetically irritating I though nothing of it until that is I discovered that they were completely immune to magic including their own.
Just to add to the weirdness when I went to Jaroo for the cure all the characters appeared after resurrection with all the buffs that they'd had, whose visual effects had lingered, restored furthermore when I attempted to remove Spell Permanency from Zaxis Jaroo killed him but failed to raise him from the dead! Fortunately I had a cleric who could although even with Restoration he still had lost some experience.

Another irritation is that after the ambush following the betrayal of a certain Monastic Brotherhood I often find that some of the chests

Spoiler

containing my clothes etc

are stuck in trees or otherwise inaccessible.