Do you mean you put them in a turner or carton upside down? If so, that's interesting.
I can think of a logical reason not to do that, though.
The chick will pip into the air cell before it breaks through the shell. If there's very much fluid left in the egg, it could run down into the air cell and the chick could drown.
It's also possible that chicks may automatically try to position themselves head up, as they can surely feel which way is up. The small end of the egg would be harder for them to rotate around in, to zip the egg open.
I don't know if that happens or not, I've never placed mine upside down, since it's just as easy to place them right side up. Did your upside down eggs pip on the big end anyway, or did they pip the end that was up? And does your hatch rate seem to be affected at all, or have you tried hatching both ways to compare?