After you file

No it wouldn't be for that.  Did both W2s box 1 show up on 1040 line 1?  Then you got taxed on it.  Did you have a refund or how much tax due line 37 on the original return?  Did you pay the tax due?  Your only proof of payment is your bank or credit card statement showing it coming out.  Turbo Tax does not pay it.  They only send your bank info to the IRS or state for them to pull it out of your account.

 

The IRS letter should say what they changed.  One thing to check is did you have excess Social Security on 1040 Schedule 3 line 11 which goes to 1040 line 31.