This refers to the color attribute setting of your Magento 2 backend only.
We have tested in our local instance with a migrated database, and the color attribute was shown normally on default Magento 2 layered navigation. Please see these screenshots of our testing instance for reference:
- Frontend: https://prnt.sc/qx7vit
- Backend: https://prnt.sc/qx7vtj, http://prntscr.com/qx7w9h and http://prntscr.com/qx7wi3.
Please check Magento 2 layered navigation guide and your setting once again.