First, in terms of the excess contribution, you will tell TurboTax who over-contributed to their HSA  This choice is up to you, it just needs to match what you worked out with the HSA plan administrator.

If you indicate that you will withdraw the entire excess (as it sounds like you will), then TurboTax will automatically add the excess to Other Income on line 21 of the 1040 IF the excess as from the code W amount on your W-2.

If the excess was from personal contributions made outside your employer (NOT your payroll deduction), then TurboTax will reduce that contribution.by the amount of the excess.

You will pay income on the excess contribution, but otherwise, you will be done with it.

As for the $4.16, was this a contribution for 2016 (even if made in 2017)? If so, tell your HSA plan administrator that this was a "mistaken contribution" when you withdraw it. See if you can catch them before they process it.

If you can, then you don't do anything about it. It will be out of your HSA (for 2016 - nothing stopping the company from adding back for 2017 - suggest that), and it won't affect your tax return.

And, although I assume you are doing this, review your contribution schedule to make sure that you don't exceed that $6,750 annual limit.