In virtually all modes on the 360, there is a decent chance that you can catch your pursuer in a smoke bomb and go to punch him, only for him to dodge your stun for no apparent reason.
In Manhunt, if there are multiple targets grouped together, the priority locking system seems very messed up. The game forces you to first attack the guy on the ground for a Ground Finish instead of allowing you to kill the guy who is actually alive. This often results in a lot of completely unwarranted stuns by the remaining targets.
Also, there are many occasions where I am locked onto a target, I hit the X button, and it decides to kill a different target that I did not have locked. This usually results in a civilian kill or an intercepted poison. Several other players have also complained that the game has forced them to interact with personas other than the one that is locked, whether it be to to kill or to stun.