Are you referring to the ones up front by the shock towers etc.? Those are access holes for mice to build homes in.
Seriously though, I wouldn't know they shouldn't be there. This is my first truck of this model and first rebuild. I bought the restoration project from another guy after he had already done the frame. I think it started life as a 2wd so maybe something to do with that. Something I should be fixing? Especially since I just got it painted and all. lol.