in my case, i always preferred to run the entire match, all stages, cold. but i ran them twice b4 changing the stage. if i had an issue with a stage, when i was done shooting the match, i would practice on that age till i ran out of ammo.
all my primers go below flush on all calibers i load on my 650. you should check that your stem is fully seated. i know from doing primer changes back and forth from small to large that it is possible to not fully seat that stem.