Why am I being called a murderer? I'm innocent _this time_!
This is just the mechanics of the game. It is similar to previous games, where guards would "investigate" bodies on the ground, and if you stood around too long they'd start chasing you. When the redcoats see a body on the ground and you're in view, they assume it was you and they will chase you. Also note that at this time, New England is still under British control. Guilty until proven innocent (if you get the chance)!