Some problems, not all necessarily bugs in the strictest sense:
(1) Disintegrate has a save according to the Arcanum game manual. In the actual game, I've never seen anything save against a distintegrate. I'd check that spell internally if I were you.
(2) I don't know if this counts as a glitch or just bad design, and if it's even fixable, but there's a pitfight on the Isle of Despair and you're not allowed to bring followers. The problem is when you have a familiar (from the highest level summoning spell). IIRC, there is no way to dismiss your familiar for this fight. So what I had to do (rather reluctantly) was walk around in a dangerous dungeon and let my familiar eventually suicide so I could continue the game. Needless to say that wasn't such a great moment. It might be the case that, by design, a familiar can never be dismissed and must always remain at your side. In that case you might have to use your judgment to determine whether the devs would make an exception for this fight or not.
(3) There is a minor glitch in which if you pick a spot on the world map very very close to a city (and don't select the dot representing the city itself), when you finish traveling, you'll get stuck in a building or on a signpost or other parts of the city's structure. It's minor though and probably not easy to fix. It also probably doesn't happen with every city. I know I got something like this to happen for Tarant but Tarant is an exceptional case, being as large as it is.
(4) Your followers will pick up all sorts of ridiculous things if they're close enough, eg boulders. This might not really count as a bug but it's still extremely annoying and unrealistic. I'd hardcode boulders at the least as forbidden. That much I think could count as a bug.