If you have an automatic fix available for this checker, you can select it from the popup list of that checker, and, then it will be applied on the fly when you register your structure (in the case of the Racemate Checker the Convert to Unknown fixer can be a possible option). Prior to registration, you can test the effect of the fix using the Check option.

If you do not find any appropriate fix for the checker, you have to modify the structure to pass the failing structure checker, or you can contact a Registrar to fix the submission for you.