You should let TurboTax calculate the excess, even if the excess it calculates seems wrong. One confusing point is that you can actually contribute to your HSA even while you have Medicare, because the limit is done on an annual basis. So if you had HDHP coverage for 6 months and Medicare for 6 months, you can contribute one-half of the annual HSA contribution limit, and TurboTax doesn't know (or care) which months you actually made these contributions in.
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