Running a Dillon, I assume you are decapping at the first stage. In that case, I suspect the particles that leave the small indentations may be primer residue that didn't all fall into the primer catch with the spent primer cups and instead were jostled loose by machine vibration as the shell plate went around and then stopped.
Decap your primer separately, or else resize and decap it in the press and remove the case from the press just before it advances to the primer or primer/charging (depending on the press model) station. Retumble the brass to clean out the primer pockets, clean the press, and try again, this time slipping the sized cases into the shell holder on the up-stroke just before the shell plate turns (or you turn it on a 550). That should end the pattern on the primers if the residue is causing it.