As an employer is over deducted $6.47 from an employee. What should I do?

Don't worry about it - when you file your income tax return you can take a credit for overpayment of SS taxes.

How did they "over deduct"? If it's because you worked for more than one company, but each of them deducted correctly, then you can report that on your tax return.

If one company deducted too much incorrectly (e.g. you were exempt from FICA but they deducted anyway), you must first ask them for a refund; if they refuse, you file form 843 and 8316.