Most annoying thing? Wrong building count.
I've noticed time and time again that the building counts get in the way of things:- The counter on the top bar often displays the wrong number.
- After I've just freed up three building licences, I can only build one new building before "Maximum building count reached"
These problems often sort themselves out after five minutes or so, but that's way too long, and just instils greater confusion about what the correct number is. Sometimes a refresh will sort out the counts, but sometimes not.
For me, this is the single biggest problem with the game as it stands.