To reproduce :

- Create a content type
- Add a field collection field, with unlimited values
- Add an entity reference field to the field collection, with unlimited values

- Create a content
- Add a field collection item, reference 1 entity
- Add another field collection item, reference 10 entities
- Save content
- Edit content
- Delete the first field collection item
- Second field collection item becomes first, but only shows 1 entity reference field