Have had no issues with CCI primers being the culprit of a misfire cartridge.
When loading 9mm, I seat to the depth of a factory cartridge of similiar bullet weight. Then place the loaded rounds in 50 round plastic holders, as found in a factory box of ammunition. I inspect for uniformity of cartridge heigth, to include the primer seating depth. you can run your fingers over the top of the cartridges as well and feel for any bumps. Any variences stick our like a sore thumb.
I also find that running a finshed cartridge through a Lee factory crimp die, also removes any "glock" bulge, creating additional uniformity and enhancing overall reliability. The FCD should also be set using a factory cartridge as a guide.
I have loaded ten of thousands of 9mm, 10mm, .and 40 rounds this way and they function in any gun.
If any of the brass you were using had crimped primers (military surplus) , then you will find it more difficult to seat a new primer into the pocket, that is if your sizing die even pushes the old one out.