Here are some card-specific problems that I've encountered recently.
Man-o'-War: Infinite loop -> crash when AI cast this. Apparently, Sloth has just fixed this. AEther Adept seemed to have a similar problem, though, and I don't know if the fix helped that one, too (haven't tested yet).
Necromancy: Crashes when the AI casts this. I replaced this with the 5th Edition
Animate Dead in the Jamuraa decks because of this.
Smoke /
Winter Orb: This is an old bug that still persists. More often than not, you are never prompted to untap that one allowed land or creature, which puts you at quite a disadvantage against the AI. The only time
Winter Orb seemed to work properly for me (i.e., I was prompted to untap one land) was in the infamous threaded input revision, which had some major issues of its own (general slowness, misbehaving prompts) - this leads me to wonder if this problem is somehow input/prompt-related?
Contagion: Crashes when the AI casts this. (Not always?) Ok, so the spell is AI-tagged and not supposed to be included in the AI decks so I replaced it with something else (functionally or thematically related, from the roughly same era) in the Jamuraa decks.