Commerce line item not referenced by the orders
This typically happens when an administrator adds a line item to an existing order via the order edit form and doesn't submit the form. The line item has already been created, but the order hasn't been updated to reference it. We refer to these as orphaned line items, and they're safe to delete as needed.

I implemented a much better approach with Inline Entity Form, which defers any write action for referenced entities until the form is submitted, but last I tried its line item support wasn't fully functional for the site I was working on. May be better now.