The 55-year-old came under fire from Scholes and Ferdinand during his final days as United boss in their roles as TV pundits.
And according to the Mail, Mourinho felt the criticism affected the dressing room and made his job almost impossible.
Mourinho is also said to have been surprised with some of the off-field departments after taking the Manchester United job.
He believed transport plans were not to the standard while Mourinho was also concerned about some of the hotels they had to stay in.
A source said: “Jose had the utmost respect for Sir Alex Ferguson and (former chief executive) David Gill. He saw them as real football people with experience in the field and knowledge in the corridors of football and power.
“That is what he thought he was buying into when he took the job. He found that was not the case with those who currently run the club.
“He feels the weakness at the top allows former players to have a greater voice.
“If the club was stronger at the top then their negative views would not have such an impact in the boardroom, dressing room or stands.”
The Mail add that Mourinho is now ‘saddened but philosophical’ after losing his job.
Mourinho was sacked by the Old Trafford giants on Tuesday, with off-field tensions compounding the club’s worst-ever start to a Premier League season.
United have now appointed Ole Gunnar Solskjaer, whose Champions League final winner sealed the treble in 1999, until the end of the season as the club undergoes a restructuring process and searches for a new full-time manager.
Norwegian club Molde have allowed the 45-year-old to make the temporary switch “back home”, but the former United striker and reserve team coach is already dreaming of a longer stay.
“When you get a job like this and they ask you to sign for six months, you say ‘yeah, I’m happy to help out’,” Solskjaer said.
“Of course, my job now is just for the next six months to do as well and move the club forward as well as I can.
“I understand there are so many managers who would love to be manager of Manchester United, so of course I’m one of them but it’s not something that we’ve talked about.
“They’re going to do a process now for the next six months.”
A packed press conference welcomed Solskjaer as a whirlwind few days continued ahead of Saturday’s first match at Cardiff – the only other Premier League club he has managed.
“I didn’t think twice when they called me to sign me as a player, and obviously this is more of an honour and privilege to be helping the club for a few months I have to say,” the Norwegian said.
“It’s until the summer now, so it’s five or six months, just help out in the meantime while the club is doing a process to get the next manager from the summer onwards.”
Lukaku looks set to miss Solskjaer‘s first match as manager. The Belgium international has been given time off and has yet to return to the club, while Alexis Sanchez is also out for the trip to the Welsh capital.
Chris Smalling pulled up injured in the warm-up at Liverpool last weekend so is a doubt, while Luke Shaw will be hoping to return to the fold. Marcos Rojo missed the loss at Anfield, as did Matteo Darmian and Scott McTominay.