Hello AXiON,
That is a strange issue, I never had anything like this happen, also you are right, the plugin should be ignored when running a scene, as none of its scripts are actually contained in any scenes. #if TOOLS to my knowledge should exclude the plugin from the project when you export it, I am unsure about its behavior when running from the editor. I will investigate this further when I have the chance, for now I assume the best workaround in your case is to disable the plugin before running the scene. Sorry for the inconvenience.