But Mourinho is in no doubt he is the right man to lead United's title challenge next season.
City are 16 points clear of second placed United, who can only take a maximum of 15 points from their remaining matches.
"City won the title because they won more points than everyone else, they were the best team".
"It's been extremely hard for me and my family on a serious allegation and subject", Rodriguez, 28, said.
"We were masters in complication, everything was complicated", Mourinho said during his post-match interview.
They won it in the last remaining seconds in 2012, and in the final match in 2014.
With the title wrapped up without kicking a ball thanks to United's shock defeat, City can reflect on a success crafted completely in the image of boss Pep Guardiola. United hope to bounce back from the defeat against West Brom against Bournemouth at the Vitality Stadium on Wednesday night.
Mourinho suggested his players might have over-reacted to the win against City at the Etihad.
"I knew that sooner or later that would be, and if I was in their position I would be very upset (if) someone said they won the league because Man United lost against West Bromwich Albion".
"I won eight titles and I am not [over] the moon because I won against Manchester City", he added. "That doesn't make me feel super happy and in my opinion affected for sure some of the people that was too happy". Everything was complicated. We couldn't play fast.
But realistically, every person in that tight corridor outside the Old Trafford dressing room knew City had effectively taken a huge step towards the title that day.
"It hurts [for Manchester City to win the title]".
Our 18-consecutive victories between August and December set a new Premier League record and we have spent a total of 240 days at the summit of the league since the start of the season.