CKEditor custom buttons do not work if Limit allowed HTML tags and correct faulty HTML filter

To reproduce:

1. Create a ckeditor plugin module or install https://www.drupal.org/project/ckeditor_bootstrap_buttons
2. Add the button to a text format (such as basic html) active toolbar
3. Turn on 'Limit allowed HTML tags and correct faulty HTML' filter
4. Load a content edit form that uses the text format

The button will then not be added to the ckeditor interface.

If you then go back to the text format and remove the 'Limit allowed HTML tags and correct faulty HTML filter' the button will be available from the user interface.

Please not that this is NOT an issue with the above mentioned module, and the same happens with all user added ckeditor plugins