Yes, it does happen, and how you approach it varies. Anytime you report something different than a form which is copied to the IRS (like both the W-2 and the 5498-SA), you run the risk of a letter from the IRS. Sometimes, this is the only thing to do - fill it out as best as you can and be prepared to explain the error on (1) your employer and (2) your HSA when the IRS letter comes.
Or you can just avoid this by contacting your HSA administrator and telling them that you made a "Mistaken Contribution" in February 2018 (the $320). In this case, you will ask them to return that $320. You will remove that from the appropriate line in TurboTax (2017 contributions made in 2018, I think), and your excess contribution will go away.
That might be the simplest thing to do.
