United suffered a 1-0 defeat to Villa at Old Trafford on Saturday, following a goal by Gabriel Agbonlahor.
Referee Atkinson added just three minutes for six substitutions and two lengthy injury stoppages, something Ferguson was unhappy with.
“The timing should be taken out of the referee’s hands,” bemoaned Ferguson. “Those two stoppages took two minutes and 20 seconds, and then there were the substitutions on top of that. That is disappointing.
“It is silly really. We are nearly in 2010. A change should be made.”
“It is a missed opportunity,” Ferguson added. “We created plenty of opportunities and we should have taken at least one.
“But this is not an easy league. If you get there, you are going to be taken the distance.
“As I always say, if we are in touching distance on New Year’s Day we won’t be far away.”
