Same here but one deviation:
Ironically, my fetch result is only missing the assets that did originate from the device where the -fetchAssetsWithLocalIdentifier:options: is called from.
I also noticed that the same local asset had a different localIdentifier when getting it via
[PHAsset fetchAssetsWithMediaType:PHAssetMediaTypeImage options: nil];
instead of
[PHAssetCollection fetchAssetCollectionsWithType:PHAssetCollectionTypeAlbum
subtype:PHAssetColectionSubtypeAlbumMyPhotoStream
options:nil]
i.e. testing these two assets with isEqual: gives NO. Whereas when getting an asset that originated from another device via these means I get identical localIdentifiers.
I was also wondering if there is some trick you would have to apply to a PHFetchOptions instance to get the assets missing within the fetch result to be considered at all (like .includeSourceTypes).