App telling me to equip items I don't have after importing

What might I be doing wrong if, after importing from the in-game addon, the best in bags tool is exporting instructions to equip items I don’t have in my bags or bank…?

An in-game export string is usually the first thing requested, so that others in the know can try reproducing the same thing.
Are you getting recommendations for gear you have not even looted in BiB… or BiS…?

You may want to look at any threshold settings you’ve made (if any), to ensure they relate to the gear/content levels you’re currently working with.