You have taken the right steps to have the excess distributed and include the amount of the excess deferral on your 2018 Tax Return.
It was just announced that an
update is currently planned for April 12th, 2019 to resolve this e-filing
issue.
You may still see a warning about the
excess contribution, but you should be able to e-file. You can check out
this TurboTax FAQ for more
information: Excess 401(k) Contribution Preventing E-filing.