Excise Tax paid on Form 5330

I have a client that did not remit some salary deferral contributions deducted from  participant paychecks on a timely basis to the plan.  The excise tax was calculated, Form 5330 filed and the excise tax was paid.  It was subsequently discovered that the excise tax paid to the IRS was over stated by several thousand dollars.  Apparently close to half the late contributions were actually allocated to the plan on time.  Has anyone dealt with this issue before?  Can the excise tax over payment be recovered from the IRS?  Thank you.

There is a section in the instructions for the 5330 titled "Claim for Refund or Credit/ Amended Return." I would start there.

Thank you for responding.