Did your league keep an updated running total of all fees owed by each owner? Were all owners able to view this total on a weekly basis?
I'm asking this because if all owners are able to view a running total of their fees, it shouldn't have been too hard to figure out that teams weren't being charged the correct amount for each loss. If nothing was said, then it seems likely that owners were hoping to get out of the extras fees and stiff the other owners. This would include the winner. In this case, I say the books are closed and be done with it.
If, however, owners had no way of regularly checking what they owed and thus had no way of discovering the error. Pony up the money and pay the man. All owners agreed before the season to pay a specific amount for each loss and should do so. Just because a software error occurred and nobody had a chance to catch it, doesn't mean everyone should get out of paying it.
Fantasy Football Junkies Anonymous meetings held weekly on Sundays... and Mondays... and sometimes Thursdays.