Reference objects identifiers are stored as '$id' in database when Embedded objects identifiers are stored as '_id'. When querying a collection by embedded objects identifier, DocumentPersister->prepareQueryValue() converts it to '$id' although it is stored in DB as '_id'. So querying for reference object ids work but embedded objects do not.

DocumentPersister->prepareQueryValue() first checks if field has TargetDocument mapping, if it is true it checks if field is target document's identifier, if this also returns true
it prepares the field as '$id' without looking at if it is Embedded or Reference object ... If TargetDocument it is a Reference object it works since Reference objects identifiers are stored as '$id' but if TargetDocument is Embedded object, query returns empty as theres no field such '$id' in EmbeddedObject, identifier is '_id' instead..

Is this a bug / issue or am i missing something?