A similar situation occurred on btcguild where some pplns shifts were paid double. The way it was handled was to deduct the additional funds from the account.
From the site:
Additionally, there was a bug last night where some PPLNS shifts were paid double. This has been retroactively corrected. Accounts which received payouts during this time may currently be showing a negative account balance.
I think the bug that happened with btct could be handled roughly the same way.