TurboTax S-Corp getting a refund

So a couple of questions:

1. You indicate that the refund is exactly the amount of estimated taxes.
2. So, did you actually make estimated tax payments under the EIN of the S Corp?
3. Or, did you make the estimated tax payments under your SS#?

Hi Rick, and thanks...

I did actually make the estimated tax payments under the EIN of the S Corp via the EFTPS site.   When filling out the TurboTax Business portion around estimated taxes, it asked amounts and method.  I chose EFTPS and was required to provide the confirmation numbers/id from EFTPS, which I was able to provide as well.

only under rare circumstances does an S corp pay federal income taxes 

the most common is when there is

Excess net passive income or LIFO recapture tax

barring those, the S corp should not have paid estimated taxes - that's why you're getting it all back.  the bad news is that unless you paid you own estimated taxes or had withholding be preppared to owe.  on top of which you would have underpayment penalties. 

So there is good news and bad news:

• The good news is that the return properly shows that you should get a refund.
• The bad news, is that these estimated tax payments should have been made under your SS#
• So what this means is that you are underpaid for estimated taxes at the individual level and will have a tax liability on your 1040 that needs to be paid.
• You will get most of this back when you receive the 1120S refund, however, you will most likely get a penalty for underpayment of estimated taxes at the personal level.
• As was noted by @Anonymous , S corporations rarely need to pay any tax since all the income or loss flows through to the individual and the tax is then paid at that level.
• When you do get a letter for underpayment of estimated tax, I would write a letter explaining the confusion on your level, include documentation that the estimates were paid at the S level by mistake.  While the IRS may waive the penalty, keep in mind that it will take months and months and months to hear back.  With all offices closed mail is piling up and it will take a long time to get through the backlog.

Thanks to @Rick19744 @and @Anonymous  for all the information.  You are right and all makes perfect sense now.  I think I had some confusion between 941 and Estimated Taxes.  Thank you both very much for your help! 

Welcome