I'm going to list a small list of pet peeves I have with Overwatch, small gameplay choices which fits Blizzard view of «gameplay should trump logic» but rustle my jimmies.
Junkrat – His bombs damage him, but his land mine do not,  even though it can be used to propel him.
D-Va – The pilot gun does more damage than the big mech gun. I mean.. wtf, just put the damn pistol outside!
Zenyatta – He is made of metal but has no armor.
Maps – You can land on some part of some roofs, but can't on others. There is no way to know before trying.  The start of Dorado is like that.
Overtime – Dozens of times I lost while stepping on the point. It's the opposite of TF2 where anyone a feet away from the point basically blocks the capture.
Oddly enough, I don't mind Hanzo arrows hitbox because I think otherwise he would never hit anyone. I do, however, get preeeeetty salty about how fast a Widowmaker can wipe a team with multiple quickscopes.