However, Mourinho hasn't taken the criticism well, and used his programme notes for the game against Crystal Palace at Old Trafford, United's 63rd match of the season, to hit back.
With an eye on the big prize next Wednesday when the Red Devils take on Ajax in the Europa League final, Mourinho has made a decision to give his first-team squad some much needed rest on the final day of the Premier League season.
Sir Alex Ferguson has praised Jose Mourinho's first season at Manchester United.
Souness also said that Mourinho is effectively "handing an excuse" to the United players for bad performances by constantly complaining about the number of games the team have had to play.
Mourinho's Manchester United will finish sixth in the English Premier League with no guarantee or possibility to the lucrative Champions league next season.
While it appears all-but impossible Ibrahimovic can play any part in the final, his United team-mate Henrikh Mkhitaryan says the 6ft 5in striker would play in the match on one leg if he could.More news: Batshuayi's late victor guides Chelsea to Premier League glory
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He wrote: "I have seen in the football media that certain pundits can not understand why our players are exhausted. It's not my fault if their managerial career was very poor". Luke Shaw has had surgery at a time when he hit his best form.
"We spent more time travelling, playing with hotels than at home because 60-something matches means 140 days in hotels".
"Don't we deserve respect for that?" Isn't this team going to play a European final next Wednesday?
"The last thing I wanted would have been a manager continually telling me I am exhausted".
He is not expected to again feature for Manchester United, but Ibrahimovic is expected to pull in the Swedes to lend their voice for his club at the Friends Arena.