Possible, I guess, but so far down the Likely List that I'm not going to worry. I routinely use a kinetic puller for small batches and generally use a shell holder as that's more convenient and thus faster.
Nah, to be honest, this just doesn't ring right. The base of the cartridge is pretty well protected in a kinetic puller. Using the supplied collet, the primer is several millimeters below the face of the cap and there's nothing flopping around which could hit it. Using a shell holder, more so - the primer is just about invisible. And shell holders are engineered to hold cases in proper alignment.
So... Maybe the primer was super-sensitive or something? That's an ammo defect and one which would have ammo going off in boxes, pockets, magazines and pouches - not utterly impossible, but not precisely common. And the jarring a round is subjected to when the hammer hits the floor or workbench is about on par with what it gets being fed by a semi-auto firearm.
Not challenging what the OP was told, but this just makes no sense.
In any case, if there's a lesson, it's the oft-repeated, usually-ignored wear safety glasses when reloading, dummy!