Manchester United chief David Gill is convinced they were poorly treated by FA.
Gill, who is a member of the FA board, was speaking in new book Champ19ns, which covers the club's record 19th top-flight title last term.
He said: "I do genuinely believe there have been some poorish decisions that, in my opinion, wouldn't necessarily have hit other clubs.
"That's not to say I'm condoning Wayne's comments, because I don't think they were correct, or what Sir Alex said (about Martin Atkinson) because it wasn't helpful.
"But at the same time, the actual punishments were harsh. We're possibly being caught up in being one of the biggest clubs and the 'Respect' agenda being there.
"What better way to demonstrate the authorities are being tough than by hitting one of the biggest clubs the hardest?"