The wife no doubt was used to getting large refunds with CTC and EIC, and it didn't occur to her to tell the preparer about the change in marital status.  Either they didn't ask, or they are like the Block franchise in Sun City AZ who told my client's new wife (he went with her) that it was OK to file HoH.  I have already told this story here, I believe -- it happened maybe 15 years ago. I didn't believe her so she went back to Block and they confirmed to her in writing that she had filed correctly. 

Anyway, best thing to do is amend her return from HoH to joint return, and explain what happened.  I would prepare an original return and mark it "Information Only, Do Not Process."  Attach it to the 1040-X so they can see where the numbers came from.