Match referee Chris Foy did not award a spot kick for the incident, a decision with which Ferguson disagrees.
He told reporters: "I think the one in the first half was a clear penalty kick, but maybe Nani made a meal of it and he didn't need to do that. He was clearly pulled back.
"Nani is not the type to dive, I know that. It was a penalty kick on Saturday. Sometimes you get them, sometimes you don't. The linesman could have helped him but didn't."
The United boss also revealed at a pre-match press conference for Tuesday night's Champions League tie against Cluj that his squad is suffering with a virus that has affected a number of his senior players.