It should not have happened no matter how the shell was being held. The shell holder also has a hole in the bottom,,,---(of course it does), just like the 3 segment holder the puller came with. The difference is the steel shell holder does not clamp the rim, it can and does move around. BUT does it move enough to allow the primer to be hit during the action of hitting on the floor? So what if it does, the primer is SUPPOSED to be seated flush, so it,(the primer), can't get hit.
Somewhat of a moot point as the OP was using the three segment case holder designed for his inertia bullet puller.
I agree in principal that a press shell holder in an inertia bullet puller should not cause a detonation of the primer under normal circumstances but over the years I have seen things happen that were not supposed to.
A loose, or less than properly tight, primer may be an extra condition that makes using a press shell holder less safe.
Anyway, here is a good read on the subject. It does not necessary completely answer the question.
http://www.thehighroad.org/showthread.php?t=578426