"It's too big a game not to get the decisions right," Ferguson told Sky Sports News.
"It balances out in that respect but I think it was difficult to see that one (Vidic's handball) but the one at the end, Clichy knew, he put his hands up in horror."
Ferguson added: "Obviously, it gives Chelsea a major chance now and that's what happens when you get these decisions.
"They got one at Old Trafford last season so that's the worry now.
"But in terms of ability - a game at Old Trafford, the supporters will be ready for it - and so will our players."
The Scot conceded his team had disappointed until Arsenal scored through Ramsey in the 56th minute.
"After that we dominated and I think we deserved something," he said.
"I think we didn't use the ball properly but once we lost the goal we were in their half most of the time."