Huh? I've never owned a Glock that had more than one serial number and it was on the frame on the underside where the rail is.
Why don't you post some pictures please?
All my Glocks have serial numbers on the
1) frame (metal tab under the dust cover),
2) the slide (under the ejection port),
3) the barrel (on the chamber side- visible through the ejection port),
4) on a sticker on the plastic case handle
5) and, in the days when fired casings were provided, on the envelope with the casings.
All of them match.
Which number is on your paperwork? Which number is on the plastic case? Sounds like the store was messing around, and got them put together wrong. They might be interested in finding the other mismatch and correcting the problem. Guns with non matching number tend to be worth less as the buyer will assume, that there was a problem and you replaced a broken part.
If the store won't cooperate, tell them you'll need to report this to the ATF. Once you shoot the gun though; it's yours.
Might give Glock a call; but not sure what they can do for you.