Excess Contribution to HSA in 2016

I have around 500$ of Excess Contribution in my HSA account from 2016. I am not eligible for an HSA account anymore ( Since Nov 2016) . I requested my HSA Bank to return that Money as excess Contribution. They told me that they will send me an updated 1099 next year ( would be for 2017) . My Question is when would i be charged the income tax on the Excess Contribution ? 2016 RETURN or 2017 RETURN.

While filing the form for Excess Contribution Refund , I mentioned 501$ rather than the 500$. Would these cause any complications ?  Turbotax is not letting me enter $501 as excess withdrawal , as i had to Withdraw only $500.