Deductions & credits

I am going to assume that TurboTax reported that the first transfer into the HSA caused an excess contribution error message.

In this case, you would be permitted to contact the HSA custodian and ask for the "withdrawal of excess contributions". If this is what happened, then you should be in good shape.

The IRS instructions for box 2 on the 5498-SA (Total Contributions Made in 2019) "Any excess employer contributions (and the earnings on them) withdrawn by the employer pursuant to Notice 2008-59, Q/A 24, available at IRS.gov/irb/2008-29_IRB/ar11.html, should not be reported as a contribution."

See Instructions for form 5498-SA.

So if you asked the HSA custodian in April 2019 to request a withdrawal of excess contributions (the first transfer), then this amount should not appear in box 2.

Likewise, issuing a 1099-SA a year later with the earnings on the excess is normal, because the earnings spanned two tax years, and the IRS lets you report them in the second tax year.

If, however, you did not get the HSA custodian to document these transactions as "withdrawal of excess contributions", then you have a problem. 

The IRS does not permit willy-nilly transfers of money in and out of HSAs. In this case, you would have to report the first transfer as a contribution (even though you took it out the next day), take it as a tax deduction in 2019, and then report the distribution as a distribution NOT for qualified medical expenses, on which you will pay income tax and a 20% penalty.

First, ask the HSA custodian if they treated the second transfer as a withdrawal of excess contributions. If they did, you are probably OK.

Note that you will receive a separate 1099-SA for your regular distributions anyway; perhaps this is what the other 1099-SA is.

However, you should talk to your bank and make it impossible to accidentally transfer money into the HSA.