I don't think @DaveF1006 is correct here.
For any employee of any company, if the company withholds too much FICA, the company has to file amended form 941 for each quarter that needs to be corrected. Did you use a payroll company or do it yourself? The SSA will send back the excess to the company when the company files the amended 941. The company should issue a corrected W-2 (W-2C) to the employee reflecting the correct amount. The employee gets the excess back from the company.
It's no different if a one-person S corp, the company amends the 941 and the company pays the employee.
Now, be aware, that turbotax is very sensitive and calculates social security to the penny, and will warn you if your box 4 amount is even 1 cent more than it should be, which is 6.2% of box 3. This is not a situation that needs to be amended or corrected, just drop the cents off the box 4 amount to stop Turbotax from complaining. This won't affect your tax return or social security at all.
