I have a field collection that contains a date and a link field called field_fc_dates. I can't always replicate it but when I click on the Remove button on a node edit form, it sometimes keeps the field data for that field collection (link, date, field_collection_item, field_collection_item_revision) but the field_fc_dates data for that node is not there so it isn't associated with a node. I am able to fix my issue by updating my view to filter (field_fc_dates) Content: Nid (not empty).

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albertski created an issue.