I've been a prius owner for a week! Yea! Does anyone else have cuts in the carpet under both passenger and driver seats? I took it back in and was told they were supposed to be there!?!
one of my communicated complaints after my test drive was of the generally cheap appearance in quality of carpet and the apparent cheap, flimsy material of plastic shell meeting the carpet in front console. I didn't look under the seat, but I personally would absorb that fact as I am willing to accept with the overall carpets.
The tech that did the pre-delivery service probably was upset that this was the tenth Prius he had to work on, when all he could afford was an echo. You should get the dealer to replace the whole carpet. Seriously, you obviously don't have package 6. The holes are for the harness that would be there if you had NAV (ECU under driver seat) or JBL (amp under passenger seat).
As dan said, there's one carpet for all Packages, and it has the cutouts to support all the under-seat goodies.