Then you did the return of contribution correctly and you are not paying taxes twice since the taxable amount in box 2a of the Form 1099-R from the traditional IRA is zero.
In addition to the 401(k) issuing a Form 1099-R reporting the amount that was eligible for rollover, they should also have issued a code-8 Form 1099-R for the portion that was the excess elective deferral and was subject to tax, the only amount that is taxable, taxable because it was excluded from box 1 of your W-2. You enter all of these forms 1099-R with the result being that Form 1040 line 4b should include none of these distributions and line 5b should include only the amount from the code 8 Form 1099-R from the 401(k).
