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 He sent three checks: one for I 130 for $535, one for I 485 with biometric for $1225, one for I 131 for $575. 

He received the returned files, but the checks weren't returned by USCIS. 

-It is weird. Normally the check should have been returned together with the application materials.

還有可能其實原因嗎？

-No because the rejection reason is incorrect payment. You may go to the bank to cancel the original check and mail the two new checks with the application materials (clip the I-130 payment check on the I-130 form and I-485 payment check on the I-485 form). Just send the original documents back to USCIS and enclose the Rejection Notice.