@andylh the NumberedBookmarks plugin doesn't do any autosave AFAIK. But there is the SaveActions plugin which does and I can see an error dialog popping up telling me my readonly file cannot be saved. This is OK unless that after closing the error dialog, a new one instantly pops up.
Is this what you meant? If so, this is a bug in the SaveActions plugin (which is a core plugin of Geany and so this is the correct project for the issue).