The holes were still within tolerance for the same rivet size. I re-primed the holes and shortened all the rivets to the correct length. And with the next rivet set, I used the tungsten bucking bar with the 3X rivet gun which worked really well.
When I riveted the hinges on the rear spar, I had the problem to with the distance from the rivet center to the hinge. My spring loaded back rivet set hat not enough space and the rivets were bent towards the hinge. Even with my other flush rivet sets (3) it did not really worked well. Finally I used the squeezer and the tungsten bucking bar to get the result within tolerance.