You have made
excess contributions to your HSA. These contributions should not have been deducted from your income in the year they were made. If you fail to withdraw the excess contributions before the due date of the tax return for the year in which you made the contribution (too late for your 2018 contributions, but there's still time for your 2019 contributions), you owe a 6% excise tax on the excess contribution. Furthermore that 6% is owed again each year until you remove the excess contributions and any earnings associated with them.
Option 1: Fix it now. You'll need to withdraw all the funds from your HSA. You'll also need to amend your tax return for last year to add the HSA contribution (and any earnings) back into your income, pay the 6% excise tax, and also pay any penalties or interest that go along with the fact that you didn't pay that tax last year when you should have. For this year you'll need to make sure that you include any 2019 HSA contributions in income even if your employer excluded those contributions on your W-2.
Option 2: Be lazy and ignore it. Maybe you get lucky and the IRS doesn't notice for a few years, long enough for the statute of limitations to expire for the years you made excess contributions. If so, congratulations! You got away with it and your HSA is probably good to go from now on. If you don't get lucky, the IRS finds out in a year or two and you owe more than you would have owed if you fixed it now.
Neither option looks like much fun to me. Sorry! Best of luck sorting this out.