been there man, my Telecaster was like that on a few frets after I bought a new neck for it, I fixed it myself, but it was lots of work, small tiny adjustments and things like that. I used some sand-paper thing on the frets and polished them down a bit, and there was neck adjustments to be done and shit. it plays like a dream now though.
but if you want it fixed fast, and not risking ruining the neck, I suggest you take it back, they'll fix it for you.
if you have really low action, you can try raising the bridge a bit. the frets might just need to be played in a bit too, who knows.
did you get the Frusciante album yet? Im listening to it right now, it's a fucking awesome album! best one Ive heard in ages