"That seems like you will be taxed in both years for the same Excess Contribution that you were refunded by your employer's HSA Administration. "
In the first year, only the actual excess contributions will be added to Other Income. This is done automatically (before you know what the earnings even are) when TurboTax discovers the excess (and whether or not you agree to withdraw it), and does not depend on entering a 1099-SA.
In the second year, you will receive a 1099-SA with a distribution code of '2'. The earnings in box 2 will be added to Other Income in this second year, but the original excess will not be (even if it appears in box 1 of the 1099-SA, it is ignored).
So the excess only is taxed in year 1 and the earnings only are taxed in year 2.
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