"How many universities are in Philadelphia?"
Translation:Quot universitates Philadelphiae sunt?
The rule says: cities belonging to 1st and 2nd declination singular (e.g. Roma, -ae or Panormus, -i) want the locative case (the same of genitive). Other 1st and 2nd declination plural cities (Athenae, -arum or Barii, -orum) want the ablative (Athen-is and Bari-is). In other cases in+ablative.
I had the same question earlier on with this module and I think that this is the case because the "preposition in + nominative case" structure is appropriate for countries only, whereas the other case (Philadelphiae, Romae, Bostoniae, Novi Eboraci etc) is used for cities and states. Not sure about the name of that case, I think it's a locative something or other, showing location, but don't take my word for it!