STYLETHREAD -- LET'S TALK SHOP!

So the other day I finally went for the addtl % off you get when you apply for the Gap CC in the store - I don't have any credit cards other than my airline miles AmEx but I was buying so much stuff that it made sense at the time.  Anyway, I went online immediately to pay my bill IN FULL and it accepted my online payment via transfer from my checking account.  Well, when I got my bill they had slapped a $50 service fee on there because apparently I put in my rounting or account number wrong - but they did not notify me before the bill was due, all of this despite the fact that the online system had accepted my number.  I would have gladly reissued my account # for instant draft had I known about the error.  I called to try to work it out (being very nice to the person on the phone), and he told me that as long as I paid the original amount due, minus the late fee, that they would waive the late fee.  Well, I did that right away over the phone and sure enough, got my new bill this month and the fee is still on there, now with a finance charge.  Any thoughts?  I hate calling customer service!  Surely I can get out of this, right?  It really does not seem fair that they would not let me know sooner as my full intention was to pay the bill in full immediately.