The IRS has not yet developed a way to handle this electronically when there is a PEO. The e-file system will not recognize the payment or refund when the same employer is on both
W-2s.
You can correct the Box 4 amount yourself before filing. Simply multiply the amount in Box 3 by a factor of 0.062 and enter that amount or 9,932.40 (whichever is less) in Box 4 (between the two W-2s).
To get a refund for the excess withholding, fill out IRS Form 843: Claim for Refund and Request for Abatement. According to the instructions mail it separately. Make a copy to keep with your return and be prepared to send copies of your W-2s with the Form 843.
To give a little background, if only one employer withholds too much social security tax they are required to refund it to the employee. The quarterly employer reports will not allow a payment to the IRS for any excess when it's one company. This brings a question as to why the PEO is preparing the W-2s this way and if they realize they need to make a change.
If there are two employers, one does not know what the other one is doing or has done nor should they. In this scenario the IRS recognizes the problem and will allow the excess to be applied as a tax payment on the 1040.
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