A shop did that with mine once, long ago. I didn't really mind because I was young and the second mount on new skis wasn't that big of a difference.
If they're new skis (and obviously you should push for whatever you can get, but) don't sweat it. 2 mounts on a ski isn't bad, and as long as you bought them new and you're not a 400 pound big mountain ripper, you should be okay.
Still, push for new ones though. That'd be sick because you'd get two pairs of rideable skis out of the deal.
Now you've learned your lesson. Always assume that the shop is basically full of retards (no offense). Measure the stuff out yourself and label it and make sure they KNOW what you want - that way they're liable