A few things I've noticed:
1. Sometimes developed strategic resources within the civ boundary, though outside of the three-city hex range, seem to disappear. [Edit: the benefit disappears, that is, the resource is still on the map with the mine on it.] I've had this happen with a 6-iron and an 8 aluminum resource...rather annoying ...
2. When an enemy unit is destroyed sometimes the graphics don't show the "final kill"...which means having to double check that the unit is actually gone....a minor annoyance
3. If you are killing off a unit for culture points ..eg barbarians....if you look at the culture numbers at the top of the screen you seem to know the outcome of the action as soon as you click, but before the graphics complete.... no big deal I guess..but a bit clumsy...
4. The game has definitely slowed down for me, particularly the early game...this can be quite annoying when there are a string of "next turn" moves with very little action required in my civ. (Annoying enough that if I'm tired, the action becomes so slow I'm afraid I might fall asleep...
...later in the game if I'm having to do a lot of planning it doesn't seem to be quite as annoying....)