Hello,
Passive 2 relates to Mu reviving. Did you mean passive 1, Fission Jutsu Y? This one creates the clone.
As was mentioned, this is not an issue or bug. This version of the breakthrough does the bonus mystery attack ONLY against non ninja units such as puppets, summons, and clones.
Thanks!

I believe he will attack the orochimaru clones, but sadly it does not matter. They are immune to death while Orochimaru is alive, and since he cannot damage Orochimaru, he isn't effective against him.