This problem only very recently cropped up; I've never encountered it before.
I have a content type (Resource) that contains a Node Reference field (pointing to Organization nodes) that allows multiple selections. Sometimes Resource nodes are updated, and Organizations are added to or removed from the Node Reference field.
Suddenly, after removing an entry from the Node Reference field, the Resource node still displays the removed Organization. If I go and re-add that Organization, it now shows that Organization twice. Remove it again, and it goes back to showing it just once.
I checked the database for that field (field_data_field_organization_ref), and the entry for that particular Organization has indeed been removed. So I can't figure out why it would still be showing.
This is occurring on two different Resource nodes, on two different websites built with the same configuration.
This only seems to happen when the entry is the first in the list; removing an entry from the middle of the list works just fine.
Flushing caches has no effect.
Is there any explanation for this?