Over Contributed to 401K. Filed taxes before Fidelity moved the money. Now need to know what to do.

I filed my taxes on April 15.  Turbo Tax identified that my wife over contributed to her 401K because she had 3 employers last year.  Was instructed to request $5111 to be removed from the account.  Fidelity stopped accepting requests on 4/8.  I filed my taxes and now I need to know what to do?