1) When you have four of the same item (ie:potions) there will be a stack of 3, and a stack of 1. When you click on the 1, it will take from the 3 stack.
Should be the other way around, so if you use one it frees up your inventory slot.
2)Forts can see past the fog of war. I've seen a friendly fort fire at an area I couldn't see
I think it's firing at the buildings, which can't move and should be fair game for siege.
3)When stunned, the Rook's trebuchet won't turn that light blueish
His various armaments fire independently, which I think means they can still shoot when he's stunned.
4)The fort's trebuchet will be defined as if there was no fog of war, even if there is fog of war
This one's a definite bug if you're saying what I think you are. Do you mean that you can see it at range without the fog of war effect?
5)If a frost wave/fire wave is cast, and the Torchbearer switches modes, the cast will continue (Don't know if that was intended or not)
It's becoming a toggle, so that doesn't really matter. You shouldn't be able to hit the toggle if you're casting, problem swolved.
6)At multiple times, the middle flag has dissapeared into the fog of war...No idea on the trigger yet, I just know it happens.
Wow, haven't seen that one before. Good find, try to get a screenshot.
Other than the trebuchet stuff I think is intentional, very good finds.