As a preface, I've experienced most of these bugs playing user created content from the Dungeon Maker. However, I believe they apply to the main campaign. Some of these have been mentioned before, but I'll include them here again.
Cantrip: Acid Splash. Can't select a second target no matter how close the 2 opponents are.
Lightning Bolt: Passes through walls. At least it doesn't bounce like it did in Baldur's Gate 1/2.
Mind Twist: Incapacitated creatures still do attacks of opportunity.
Follow Up Attack: does not work with Versatile Weapons wielded with both hands. Heck, since versatile weapons are generally lighter than full on 2-handed weapons, this seems to be a definite oversight.
Dragon breath weapons. Passes through walls like lightning bolts.
Fire Osprey. Should always be lit. Makes no sense to attack a fire-based being at a disadvantage because you're in the dark. Also, when getting the "On Fire" effect from the osprey, it says it's due to a fire spider.
Large creatures and cover. I don't think cover is working properly when fighting large+ sized creatures. I was on a ledge fighting a Sorr Akath abomination, who was also on the ledge with me. There was a "bump" in the well (a recessed pillar so that only a quarter or so of it projected beyond the wall). I got a -2 penalty to-hit because of it. Maybe if it was a small creature that would have made sense.
Large creatures occupying the same space. I once had 4, yes, that's right, four, ogres occupy the same space. I just recently had 2 Sorr-Akath abominations occupy the same space. Hard to know which one you're targeting on top of the fact it shouldn't be physically possible.