The Dutchman worked under Sir Alex Ferguson at Old Trafford for two spells, the latter of which saw him in the position of assistant coach.
Meulensteen, who left United in the summer on the back of Ferguson's retirement and the appointment of his successor David Moyes, admits he did not expect to see reigning champions off the pace this season.
Moyes' side currently sit seventh in the table, 15 points behind leaders Arsenal and when asked if he was surprised by United's woes, Meulensteen replied: "Yes - because they have got good players.
"I know them inside out and I know the players, they have still got world-class players and that is what you're going to be up against.
"Let there be no mistake, they are still a fantastic club with a very, very good team. It is just the fact they aren't firing from all cylinders and they will, it is just a matter of time.
"It is a club I worked at for many years, I love the club and the people there so of course I would like to have seen them done better - all of the players know that."
Meulensteen was not the only member of backroom staff to leave in the wake of Moyes' appointment as the former Everton boss looked to bring in his own team, with the likes of Mike Phelan and Eric Steele also departing.
Moyes has said he feels the club is now in transition and Meulensteen backed the United boss to build a new team capable of challenging for honours once again.
"I think you always do that (rebuild) as managers," he said.
"Sir Alex Ferguson did it over 26 years, he built three teams, four teams and the only thing different is that he thought it was now time for someone else to take that process on and that is what has happened."
Moyes will now welcome Meulensteen and bottom side Fulham to Old Trafford on Sunday but the Dutchman will not be thinking what might have been had he stayed on as part of the new-look United.
"What has happened has happened," added Meulensteen.
"I have moved away and I'm in charge of Fulham. Decisions have to me made, I have moved on and I'm fully committed to Fulham Football Club.
"We had discussions and they resulted in the fact that I decided it was better to move on. We came to a mutual decision that we thought it was better for myself and David for us to part ways."