I have found three bugs, but can't necessarily recreate them 100% of the time.
(1) Random CTD. Can't put a finger on it, but it may be my drivers or the game. Who knows!
(2) Save games not always correct. I saved a game mid-mission because I had sunk a ship and was being pursued by others and knew it'd probably take more than one try. Anyways, when I saved I was surfaced, but when I reloaded (after I died) I was submerged, and my crew was still on the deck with no ill effects. See here:
(3) Sometimes the "up" key gets stuck while in external view, so the view will constantly move "forward". Even if I go into the ship and then do an external view again. It seems to happen at times after I have been holding down the Shift key to accelerate the movement. Really annoying. Have to save and exit out and restart to fix it.
Well, hopefully these can be fixed in the next patch. I also notice the system hangs a bit if you are at 1024x time accelration and enter a harbor or nearby ships. But then that may be because it is trying to load a bunch of stuff all of a sudden at once.