Funded traditional IRA with $11K ($5.5K for '16 and '17), then used backdoor Roth conversion. How to avoid TT from categorizing the '16 amount as '17 over-contributions?

In other words, I've been taxed on the $5.5K contributions corresponding to 2016 because I do not know how to tell TT that the funding happened in 2017, but the contribution went towards 2016