A overwrite ( An index operation on existing document ) or an update operation also does delete in background.
Due to immutability of segments in Lucene index , deletion operation is not exactly possible easily. For any change to the original document operation , like reindex or update , it needs to delete the document , mark it as deleted and create a new document with the change , in the background.
You are seeing this delete because you might have used UPDATE API or written a document to a doc ID which already exist.