It's explained in horrific detail in How do comment @replies work?How do comment @replies work? but the gist of what you need to know here are thus:
If there are only two users leaving comments, it is not necessary and the system will know to notify the other party. Therefore it will strip it as a courtesy of clean comments.
Use the @ notation when there are more than two users leaving comments on the same post.
If you need to @ ping another user leaving comments on the same post, don't do it at the front of your comment. Work it in naturally somewhere in the middle or end.
The owner of the post is always notified and it's pointless and noisy to @ ping them in the comments.