After entering the excess contribution the way they are, you will get a prompt from TurboTax saying that you have an excess contribution. This is along the end of other information regarding you HSA.
Then you will see a screen that actually asks if you will be removing the excess contribution prior to April 17, 2018. Of course, you already have removed it, so your answer is Yes.
This will clear up this problem that your employer has created and set you back even with the IRS.
If while doing this, you get stuck, please let me know so I can help you take care of the excess contributions.
