I followed the instructions in "Steps to Take to Remove an Excess Salary Deferral." However, Smart Check flags that I have over-contributed on my W2's and doesn't associate that the steps taken in the above instructions resolved the problem. How do I tell TurboTax that this issue is resolved? Is there another step I need to follow?
You have taken the right steps to include the amount of the excess deferral on your 2018 Tax Return.
At this point, you are running into an e-filing issue within TurboTax. An update to fix the issue is expected to be released around 4/5/2019. You can check out this TurboTax FAQ for more information: Excess 401(k) Contribution Preventing E-filing.
Be sure to sign up for updates to be alerted as soon as there is a solution. If you do not want to wait for an update, you have the option to paper file your tax returns as this is only an e-filing issue.