Mouse Cursor Stuttering:
The most annoying problem I have encountered has to do with mouse movements. Whenever I am selecting character groups (the little 3x3 set of circles with each of the units listed), my mouse gets very jumpy and does not respond well to movement. Tried multiple mice and the cursor doesn't skip anywhere aside from that small portion of the screen. This leads me to believe that it is definitely a programming bug.
Failed Research:
I don't know if this is a bug or I was just doing something wrong, but none of the refined technologies would successfully research. I would research the technology and it would finish, but when I look at the list, the technology still wasn't researched. The problem seemed to only affect technologies that were called "Refined X" (X=diplomacy, economics, education, agriculture, production, training, defense, attack, arcana, channeling).
Game freezes:
The game seems to pause randomly, and I can no longer click on anything or do anything. It is almost as if it got stuck on a particular AI process. Sometimes waiting 2-3 minutes is enough. At that point, some sort of action occurs (enemy destroyed a resource) that requires me to click OK; however, sometimes it just stays there forever.