"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.
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