A few things I've noticed:

1.  Diplomacy tree is unfinished.  Unlikely Friends, Pariden's Ally, and The Third Race don't seem to do anything.  I haven't gotten up to Dance with Dragons yet, but I'm assuming it's the same.

2.  Teleport Friends sometimes results in mana being spent and stack staying exactly where they are.

3.  Archer unit arrow tracking sometimes tracks arrows coming in from outside the battlefield.

4.  Pause after Sovereign attacks.  My Sovereign can attack twice, but when I try to do so using archery, I have to wait 5-10 seconds before I can make a second attack.

5.  Goodie and Quest huts are often un-attainable.  Mousing over them shows their stats, but walking on them does nothing.

6.  Neither of the Moonstone quest guys are working for me.  Every time I walk onto their building it gives me the same quest dialog, however even when I return with 10+ moonstones in my inventory, they give the same text as the first time and will not allow me to turn anything in.

I'll post anything else I run into along the way.