I think you should be able to choose what kind of building you want to upgrade, sometimes you want the next level of that building, but the AI builds another level 1 right next to it.
Ok, so here I was thinking: Hey, thats a pretty cool sword i got from the merchant it cost me just 3000, lets farm some stones to upgrade it even more!!!
[1 hour later] hehe lets get this shit done :DDD
WAIT WHERE IS THE FRICKING SWORD??
so thats how i closed the game and never will open it again