Murphy's law says "If it can go wrong,it will" I suppose its possible some combination of dies and shellholder could result in excessive head clearance.
That said,the ,manufacturers of reloading tools generally make dies and shellholders compatible.
We SHOULD be able to use a Lee or RCBS shellholder with Redding or Forster dies without sizing the brass out of SAAMI spec. In other words"Sizing brass too short " for a SAAMI chamber "shouldn't" happen.
But I believe in Murphy's law. IMO, it may be best to buy "same brand" shellholders with your dies and keep that shellholder in the die box. I cannot say I'm that meticulous.
What I DO is buy a Wilson type bushing "Cartridge Headspace Gauge" and verify my tools are sizing brass to SAAMI limits. I can also use it as a case comparator (with a mic or calipers or height gauge) to tailor cartridge head clearance to a particular rifle. Note these are NOT an ammo checking "plunk gauge".
I cannot imagine how commercial dies and shellholders wou;d create a problem such as you describe unless they were modified.
There are only so many ways primers fall out.
Among them,
1) Gross and dangerous overpressure (Getting your powder charge weight out of an old PO Ackley book for a 30-06. The H-4895 changed "Why does this thing kick so hard? And the primers fall out. Yeah, Dads old hunting buddy reloaded them the same as in the 1960's) )
2) Defective or improperly annealed brass. Soft cases or oversize pockets(Fire Sale Brass?)
3) Handloader created issues. Processes gone wrong, such as "uniforming pockets,reaming pockets,decrimping pockets annealing brass,etc. I'm not saying these processes are wrong. They can be messed up.
4) Brass is just ready to retire. Sometimes after 3 or 4 loadings, sometimes 20+.
5) Somerging else.