>>>What should I look for to solve the 'problem'?<<<

Try to isolate the variable.

Shoot the remaining offending ammo in other rifles.

Shoot other ammo in the rifle with the pierced primer.


If you had a single bad primer forget it and go on.

If the ammo is systematically bad it will pierce in other rifles.

If your rifle pierces other primers The rifle needs attention.


(If you were using reloads and pierce a primer you have an entirely different problem)