I've made this list, it contains problems for BG1 and BG2 as well. (perhaps even BGEE) Some of them was posted before, and some of them are pretty well-known but it wouldn't hurt to mention. Sorry for my bad english...
1. The spell „chant” has blue icon colour in the priest scroll while in game it has white.
(Not sure if it is the only case.)
2. The alhoon has a nice hobgoblin voice set.
3. Casting Failure problems:
-There should be an icon for casting failure (miscast magic?)
-Shield of Balduran does not save you from the effects of anti-magic ray (also reflecting isn’t always working sometimes it just absorbs)
-Spell Shield Protects against beholder anti-magic rays without being canceled out. (not a bad thing)
-Wizard Slayer’s attack WILL cause magic failure even if you are protected with stone skin, mirror image etc. And there is no information how long it will last or how can it be removed.
4. Turning to Slayer won’t be removed if someone joined later in to a multiplayer game. Altough if someone tries to use it, the main character will be affected.
5. Simulacrum problems:
-duplicates got no casting limit, neighter in numbers or in race (Keldorn-copy with Vailor’s helm is able to summon multiple devas same goes for Wild Mage-copy with Nahal’s Reckless Dweomer and planetars)
-Duplicates has a bad tendency to speak random nonsense (voice for successful trap setting)
6. Time stop (and time trap?) doesn’t stop spells to wear off.
7. Importing character from BG1 save games cause bugs in BG2
I tried this only with the Final Save which is generated automatically after killing Sarevok. Two problems happened:
-The character will loose the biography and will have multiplayer biography (starting with: "You have been the friend of CHARNAME...")
-If the difficulty settings are at lowest (or lower than normal I guess) the HP will recalculated but I don't know how. For example I had a level 9 mage with 18 con (so 54 HP) after imported I've got 37. This won't happen though in normal mode.
-I've just noticed that if you try import in tutorial all the CHARNAME-s in the biography will be empty while in single player it will be the name of the character.
-More problems with calculations if the character is under the BG1 xp limit.
8. Well known problems with Jaheira and Harper Pin (I never got one without romance not even with baldurdash fixpack)
9. Missing wolf paperdoll with wild surge 47. (perhaps 13?) (16 and 83 are not tested)
+1 not a bug, but wisdom's "Mag Def Adj" should be in the game like it is in the original bg1 ang bg2 manuals