Worst case .. stop Kodi and rename /storage/.kodi to /storage/.kodi-old and then restart. You now have a clean install. You can stop Kodi and move back things you need (sources, thumbs, DB files, etc.) but redo add-ons .. without tubed.
FWIW I have both YouTube and Tubed installed and never see any problems with either of them, so it sounds like something got messed up.