Wait for the letter of explanation to come for the answer to your question. Or have him log into his online IRS account and/or use the Where's My Refund? tool. My guess would be they reduced your refund but then also added some interest payment for the delay in the processing time ... so it may be a combination of things.
https://www.irs.gov/refunds
https://www.irs.gov/individuals/get-transcript
