Oh, dear! I hate sticker shock like this! Most likely, you were in partial suspension as a result of the failed payment arrangement. The restoral fees would not be generated until the lines were reactivated. What confuses me is that now T-Mobile's system requires restore fees to be paid with the past due balance so I'm not sure how they ended up being billed like this. Did your rep say anything about "waiving" the fees?
Just so I'm sure, you are referring to the $20 per line restoral fee and not the standard late fee?