Permit fees are not usually included- if for no other reason than various government agencies keep changing, or adding to, their fees.
Such fees are also, when you get down to it, the responsibility of the property owner. I (In a "turn key" operation, this would also be the GC).
So how to resolve a dispute. Simply don't call for an inspection until you've been paid. The permit is in your name- only you can call.
The GC you describe is, at the minimum, unprofessional. You're probably better off working with someone a little more, well, competent.
