"it had me do the HSA credit." First, there is no such thing as an HSA "credit". I assume that you are referring to the HSA interview, where you are asked a series of questions about your HSA.
Yes, some or all HSA contributions are listed in Box 12 on your W-2 with a code of W, but you have to go through the HSA interview in order to establish that you had HDHP coverage (the W-2 doesn't tell us that). In addition, TurboTax has to determine if you made excess HSA contributions, which, once again, the W-2 doesn't tell us.
"ask how much my employer put in" - where does it ask this? It asks you how much your "personal" contributions were, but as dmertz noted above, no part of the code W amount should be entered as a personal contribution.
"it basically then credits the whole amount back to me" What does "credit the whole amount" mean? You mean, it increases your refund by the code W amount? It can't. And surely you don't mean that you are getting a credit for this. As I said, there is no HSA credit.
So, please tell us,
1. your code W amount
2. the amount of "credit" you think you are getting.
TurboTax asks if the employer told the employee about any "other" amount contributed to the HSA, meaning either an amount not included in the code-W amount or an amount included in the code-W amount that was for the prior year. Nothing was mentioned that indicates either of these situations apply, so the only dollar entry should be the code-W amount entered in box 12 of TurboTax's W-2 form, no dollar amount entered anywhere else with regard to contributions made through the employer.