I think the question is why use the gun at all. They had the kunai there. If Beat was down for the count from the kunai, it would be pointless to shoot him and then stab.

The only reasons would be if Beat wasn't down and it was the only weapon they had, if they wanted to make it look like Beat was still fighting, or if they wanted to frame Gundam. But based on how he's acting, he knows something about this, so I doubt it's the last one.