Did the program include the worksheet for the General limitation on tax credits and the 2 worksheets (A & B ) for the limitations related to the form 8812? If so, go into the program and make sure that those were calculated correctly when the return was submitted, and that the return submitted matches what you believe are the current correct calculations. In other words, make sure that there wasn't a program update of the calculations after filing this return to verify that you are looking at the return that was actually filed.
I once had changes that luckily didn't affect the final outcome of the return, and when I opened the return within the program it didn't match the pdf of what was filed for the client.