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In the Organization Vault, all the ciphers that have no Collection assigned do not show under Unassigned section. The ciphers are only visible under "All items". From what I can see the API correctly returns such ciphers with CollectionIds set to [] and when editing the collections assignment, Vault correctly displays that cipher is in no collection, it's just that filtering misbehaves for some reason.
Could be that the upstream API actually returns Null instead of [] or there is some extra field indicating no collection assignment, that we don't send?