OP - Need the details of your ticket(s). What was your exact itinerary (including marketing & operating carrier of each segment), were you on one ticket or two tickets (not PNR's, but tickets) and, if on separate tickets, what were the checked baggage allowances for each ticket.

If on one ticket, US law provides that the base (not including waivers for status) checked baggage allowance of the marketing carrier of the first segment applies to the entire ticket.

Thus, the exact ticketing details are critical and it is not worth complaining or asking for advice until you have provided details.

Also, as a matter of interest, who asked you to pay the fee and where did this occur?