Yea pretty sure you can only get it back on the 1040 if you had withholding over the max due to 2 (or more) different employers. But if he's under the social security limit and just had too much SS withheld, then it has to be handled through employer and 941's amended to reduce it. The payroll providers typically just do whatever you ask and claim no responsibility on anything so I would expect them to charge him for the amendments. Even though they filed "wrong" numbers on there, they were just doing what he asked.
It seems weird though because it should have shown up as an overpayment on the 941 because the 941 has you multiply the wages by the percentage to calculate the tax, and then it has the line for payments. The payments should have been more than the tax due and refunded/applied forward.