I have been on a Baldur's Gate vacation for the past 2 weeks and have played a good deal with the 2.5 patch. I have noticed several new problems. I am playing with the SCS and item randomizer mods, however, so a few problems may be related to these mods and to the release of SoD. As yet, I have not purchased SoD or played it so I do not know if some changes in expected behavior are a result of this expansion.
1) Multiple anomalous damage results. NPCs and monster doing more damage than is possible. For example, in a recent battle, bonus damage was applied on a monster's initial attack as though the setting were insane. His other attacks did normal damage. I do play on insane sometimes, but in this case, the setting was hardcore rules. It appears that the monster in question was also receiving an extra attack per round as though the setting had slipped in LoB for this initial round of the battle. The setting had never been changed in this game and had been on hardcore from the beginning. Also, characters do more damage than should be possible at times. I have seen multiple instances of this: too many to list.
2) The new rules for bard-song and the range on the Blade-Bard song and HLA bard-song are terrible and make bard-song nearly useless, removing the primary utility of the class. This was as poorly considered change, in my opinion. If the idea was game balance and to remove late-game exploitable stacking bard-song, the best change would have been, in my opinion, to limit clones of any type to 1 per caster and script the clones to dispel if they move out of visual range of the caster (if this is possible in the Infinity Engine). This would remove other late-game exploits as well involving clones.
3) The issues of characters stacking on some maps has already been mentioned. In one case, the stacking resulted in Jaheira disappearing from the map completely and permanently. She was stunned, while stacked, I believe, and when I was able to separate the stack, she was gone from the map. I still had access to her inventory and character screens via the party roster, but she was nowhere to be found.
4) My recent completed game of BG1 did not generate a final save. I killed Sarevok 3 times, and each time the game continued with my party trapped in the Temple of Baal. This is not a major issue, because I created a save after Sarevok was dead and can import my Charname from that save to BG2, but it is nice to watch the final video after completing a hardcore run without dying... lol.
5) Did you change the hitpoint roll rng? It seems that hit-point rolls for PCs are all above average. All of my characters hit points are well above average.