Was the son's return e-filed, or paper filed?  If paper, IRS might not have noticed the box that was checked.  If electronic, are you sure the copy you have is how it was filed?  Does claiming himself make a difference in his tax?  Have you checked whether the refund he received, matches what is shown on the copy?  

As others have said, first name makes no difference.  I don't file using the first name on my SS card.