The returned Roth contribution is not taxable, only the earnings are. It sounds like your 1099-R is not correct because only the returned earnings should be in box 2a per the IRS 1099-R instructions that the Roth administrator is required to follow.
https://www.irs.gov/instructions/i1099r
Roth IRA.
For a distribution from a Roth IRA, report the total distribution in box 1 and leave box 2a blank except in the case of an IRA revocation or account closure and a recharacterization, earlier. Use Code J, Q, or T as appropriate in box 7. Use Code 8 or P, if applicable, in box 7 with Code J. Do not combine Code Q or T with any other codes.
However, for the distribution of excess Roth IRA contributions, report the gross distribution in box 1 and only the earnings in box 2a. Enter Code J and Code 8 or P in box 7.
**Disclaimer: This post is for discussion purposes only and is NOT tax advice. The author takes no responsibility for the accuracy of any information in this post.**
