Native mode is broken due to a bug since Firefox 71, as you can read in the about section.
In custom mode, if you are using multiple highlight colors, and after highlighting a series of words with different colors you want to remove one of them, just right-click on any occurrence *of this color* and select "Remove highlighting" (instead of right-clicking at a random location in the page). For any other issue that is not encountered. For other issues, that are not encountered by the majority of HightlightAll users, please use my contact page to explain how they occur and provide details so that they can be fixed.