really not sure how this happened

This happens because convert rules are active and a mod (supplementaries i think?) makes shulker shells into wearable helmets.

You can blacklist either the shulker loot table or remove the equipment type from shells via config. I may look into making that a default config option.

It happened naturally, I'm not really sure if it generated in a box or dropped from a mob though

Shulker shells are now set to type NONE by default.