That's actually a good thing. I ALWAYS overpay my quarterly taxes. That way, I am one hundred percent guaranteed that I will get a refund when I file my tax return. So nothing to worry about. Your overpayment will be refunded to you when you file your 2016 tax return.

Do I need to file 941X to correct this error?

What error? It's not an error. Just an overpayment. You'll get it back when you file your 2016 return, which you're probably getting started on now. You asked "can I ask for a refund", and the answer is yes. You will get that refund when you file your 2016 tax return, AUTOMATICALLY. No special action required on your part.

I am a monthly depositor, since I am overpaid on Oct and Nov, do I still need to make payment for Dec online? My Dec balance is 0, but the online system won't allow to put into 0 as payment.

So make a $1 payment then.

I received a check back from my overpayment. What process do I follow?

It appears you made a mistake with your computation which could be the reason you were issued a refund. 

Go ahead and deposit the check. Typically, you should receive a notice explaining the reason. 

You will need to amend your 941 and correct the Forms W-2 /W-3 respectively to match the IRS record.

 

See additional information in the IRS link below:

 

Correcting Employment Taxes

 

@ssanders4