What kind of bindings and what kind of skis?
It could be that somebody messed up positioning the drill jig, but that's hard to do (they're supposed to be idiot proof). If they're not centered right, take them back and ask for a new pair of skis. That's just plain wrong. I think someone either did not pay attention, or hoped you would not notice.
I recently mounted some Markers on a pair of K2s without a drill jig, and it would have been impossible to get it wrong. There was not enough width on the ski to be off by more than 1mm (or else I would have been drilling/screwing into air).