First, you do not (and therefore TurboTax does not) track your HSA totals on your tax return. Although your HSA contributions and distributions are reported on form 8889, your tax return does not know (or care) what the amount is in your HSA at any given time. How could it, because the money in the HSA is earning interest and dividends and whatever, and this is not ordinarily reported on your return.
Again, as I noted above, an excess contribution is the result of contributing to your HSA more than your annual HSA contribution limit - it has nothing to do with how much you may have spent out of the HSA. HSAs are not done the same way that old FSAs were done.
By your description, I am inclined to believe that you did not finish the HSA interview in TurboTax. It sounds like you did not tell TurboTax if your spouse had HDHP coverage and for how many months. Properly answering the questions about HDHP coverage allows TurboTax to calculate your annual HSA contribution limit. Since you say that the excess is the entire $2,299.88, it seems that your calculated contribution limit is 0 (zero), which suggests that the questions on HDHP coverage were either not answered or were not answered correctly.
Be sure to go all the way through the HSA interview, and if you have any additional questions, please come back and ask them.
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