Did you mean to say that you had $3,350 of excess contribution removed (not $3,040)? Removing only $3,050 still leaves you with a $300 excess contribution. (I assume that you are under age 55, otherwise $3,050 would have been more than your excess contribution.)
When TurboTax indicates that you have an excess contribution, allocate all of the excess to you (not to your wife), then indicate the amount that you will have had returned by the due date of your tax return. TurboTax will remove from the amount on line 9 of your Form 8889 the amount returned.
Assuming that the return of contribution was done in 2021, you'll report the code 2 Form 1099-SA on your 2021 tax return and any attributable earnings that accompanied the returned contribution will be taxable on your 2021 tax return.
