Thanks guys! I checked the airflow direction of the filter and it looks like it's seated correctly. I don't think it was sabotage, I've been to this dealer a couple of times and they've been alright so far.
As far as debris is concerned, I'll take it apart as soon as I can, and see if there's any easy fix so I don't have to involve the dealer. Otherwise I'll be bringing it back. After owning the car for the last 4-5 years I doubt it's a coincidence that the sound started the day I brought it in, they probably accidentally nicked the fan, or something fell in there.
Thanks everyone for your input! Very much appreciated.