Cleverley left the Reebok Stadium with his foot in a protective cast after being caught in a tackle by Bolton skipper Kevin Davies.
Even Cleverley fears the worst, which comes at a bad time given the 22-year-old has just broken into the England squad.
The injury cast a shadow over United's ruthless 5-0 triumph and left Ferguson biting his lip.
"We think it is a broken foot," said Ferguson.
"It is unfortunate but we expected it. It was a bad tackle."
Davies was not cautioned for the incident but shortly afterwards picked up his 100th Premier League booking for felling Patrice Evra.
If the worst is realised, Cleverley can expect to be out for around three months.
The injury did not prevent United maintaining their sensational early season form, with Wayne Rooney becoming only the fourth player in Premier League history to score hat-tricks in back-to-back games.
It took Rooney's tally onto eight for the season, more than 18 Premier League clubs have so far managed, the exceptions being United and Manchester City. It also moved him level with Sir Bobby Charlton on seven three-timers for the club.
It is a far cry from Rooney's poor form of 12 months ago, with Ferguson believing the trigger has been his number one striker's new-found maturity.
"When players get to their mid-20s, there is more thought in their game," said Ferguson.
"Their timing is better. Wayne's presence is good and he is looking fantastic."
Rooney was joined on the scoresheet by strike partner Javier Hernandez.
Handed his first start of the season, the Mexican took just four minutes to open his account, nipping in front of Gary Cahill to touch home Nani's low cross.
Rooney then took centre stage, netting twice before the break and completing his three-timer after the interval before Hernandez rounded off another amazing win, coming just a fortnight after United scored eight against Arsenal.
"Hernandez's movement, speed, imagination and presence within the game was terrific," said Ferguson.
"He is a menace to any defender. Over the years the second season for players can be hard. But I never had any doubts."
Ferguson will check on Evra, who took a blow to the knee, before finalising his squad for Wednesday's Champions League encounter with Benfica in Lisbon, although he expects to be without Jonny Evans, who was forced off with a hip injury.
"Without the goals, Jussi Jaaskelainen had two saves in the game," reflected Bolton boss Owen Coyle.
"We had double the shots, treble the crosses and David De Gea made some great saves.
"We paid the price for probably every mistake we made in the game but the Premier League is ruthless."
After four games, the table has been annexed by the two Manchester clubs, who have yet to drop a point between them.
"They are both terrific teams," said Coyle.
"City have spent £300million since they came in and United spent enormous sums of money in the summer as well to bring good players to the club.
"There's no doubt when you have that wealth at your disposal it makes it easier to get world-class players in your team.
"The form they are in just now, both sides, they are pleasing on the eye and scoring lots of goals.
"It's going to be a fantastic title race this year again, no doubt about it."