I had that happen last year and almost again this year! That is a very dangerous button to hit. It does hurt and hopefully you can get passed screening if not it's something to remember for next year to always check before submitting.
Yeah, RPG Maker MV's delete unused files doesn't take into account stuff that's used for plugins. I went through my project and manually removed the RTP stuff I didn't need (even then I didn't dare touch the sound effects or battle animations just in case).