If you took the missed 2015 RMD in 2016 then it was a 2016 distribution that must be reported and taxed in 2016, not 2015. Both distributions taken in 2016 must be reported on your 2016 tax return.
Only the 5329 waiver should have been filed for 2015. If you reported the RMD taken in 2016 on your 2015 tax return without a 1099-R then you need to amend 2015 and remove it, which will probably result in a 2015 refund to cover the tax on for 2016 when the distribution was actually taken.
A IRA distribution can only be reported in the tax year actually taken and then only on line 15 on the 1040 form, never on line 21.
**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.**
