The Champions League encounter was turned on its head after Nani's dismissal.
Asked whether Sir Alex had spoken to Turkish referee Cuneyt Cakir, Phelan responded: "I don't think he is in any fit state to talk to the referee about the decision. I think it speaks volumes that I am sat here and not the manager of this fantastic football club. We all saw and witnessed a decision that seemed very harsh.
"We had a massive audience around the world with people watching in how many countries I do not know, and everybody will be sitting there wondering what happened. A great performance was marred by one decision."