When moving an Actor that is referenced in the source level, UEditorEngine::CopySelectedActorsToClipboard will try to select the Actor for delete which will pull the \"Delete Referenced Actor\" dialog. If the user selects cancel to abort the move, the following steps complete and this results in duplicated instances of the referenced actor (Source and Dest levels). The problem seems to be that CopySelectedActorsToClipboard doesn't care for the return value of edactDeleteSelected so it can't abort the move operation.
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-374670 in the post.