"My 1099-SA box 1 includes distributions from ALL the funds I deposited in 2019 including $3090 that was applied to 2018's HSA. "
Actually, even though it seems like it does, it doesn't. The 1099-SA reports on distributions, as you noted, not contributions, which is what causes the excess contribution error message. It appears that your distributions just happened to match your contributions for the last 2 years. But the 1099-SA has nothing at all to do with excess contributions.
Note that the HSA is persistent, that is, amounts unspent in one year carry over to the next year. That is why it is perfectly possible to spend more on medical expenses in one year than your contributed in that year.
Was the $3090 that was applied to your 2018 return a "personal" contribution (i.e., direct to the HSA not through the employer)? If so, you DON'T report it on your 2019 return; you should have reported it on your 2018 return.
So just take it off; it doesn't belong on your 2019, and that will fix the excess contribution issue.
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