Here are a set of those brackets, they all look pretty different from one an other. A couple of these had some "ripples" in them too. I checked that against another set I have on a frame and those didn't have any so yes it appears they are not suppose to have them. I have to say it is very common for a part like that to have ripples in the metal as they were a quick stamping and not suppose to be perfect, just strong enough to hold a running board was all it was suppose to do. You can see that there is even a little twist in some of them.
But anyway, putting the running board on and making it level and all is really what matters. Are your bed and rear fenders on?