TractorBoy
Prince
My biggest little annoyance is when I click on a unit to give it an order, and then I end up giving the wrong unit the order because the game decided I need to give someone else an order next instead.
That takes the cake because it should NEVER be happening, and yet it does and can cost you a unit, or a settler, or worse: a battle.
I have a lot of patience when it comes to playing CivV but the above mentioned pushes me to the limit.
Playing Vanilla I hate it when a gifted Great Person is ice locked for the duration of the game.
Sending a worker, settler, GP or military unit 3 or 4 spaces over land and it decides to take the sea option and gets killed by a barbarian naval unit. If the sea option was quicker then I would consider it to be my own fault, but invariably there is no advantage in doing so.
Sending a unit a few spaces through a mountain pass, some other 'friendly' unit appears in the narrow route so the ordered unit decides to take a 30 turn detour round the other side of a mountain range.