My take:
Reverse-Flash is Future Wells. So he was beating up his past self to give himself the perfect alibi.
Remember they pointed out in that same scene that Reverse-Flash has an even greater healing ability than Flash. So clearly Present-Wells is not going to instantly heal the wounds he received or else it would be a dead giveaway. Ergo, he doesn't have his powers yet.
Present-Wells is being secretly aided by his future self. He's a patsy. He's playing with himself.
Reverse-Flash is Future Wells. So he was beating up his past self to give himself the perfect alibi.
Remember they pointed out in that same scene that Reverse-Flash has an even greater healing ability than Flash. So clearly Present-Wells is not going to instantly heal the wounds he received or else it would be a dead giveaway. Ergo, he doesn't have his powers yet.
Present-Wells is being secretly aided by his future self. He's a patsy. He's playing with himself.