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No, the most relevant thing was staring me in the face - you are using Online as you said all along, but I test in the CD/download version (much easier to test this way because I can see all forms at any time).

What this suggests to me is that I have reproduce your entries in the Online version, in case it works differently. Historically, this has not been an issue in the HSA processing, but now that I know this, I have to rule it out.

When I make a test similar to yours (must not be exact because the excess is somewhat different), I see a message that may be easy to misread"

You see the $6,517 total? There is a subsequent reference to $3,619. This is because the $7,300 Family annual HSA contribution limit is shared between the taxpayers (something you realize now). TurboTax allocates the $7,300 is it see fit. At the end of this processing, there is $3,619 that could be shared one way or the other. So TurboTax is asking how to do it. 

The excess in my case is $6,517 on two screens hence no matter which bullet point you pick (you, your spouse, or both). However, the amount for each person may change depending on how the Family limit is split.

Please go back and see if this is what your tax return really says.