United went behind following Joe Bryan’s superb opener but Zlatan Ibrahimovic equalised with a low free-kick.
Bristol continued to threaten and scored a last-gasp winner via Korey Smith to book their place against Manchester City in the semi-final.
Mourinho believes Bristol got ‘lucky’ with their result but feels his players did not have the same motivation as their Championship opponents, despite being advised before the game.
‘For them [Bristol] it was a big day, big teams against teams of lower division this is always a risk, and you advise, advise, advise, but in the end the players are in a different level of intensity of motivation than the opponent, and sometimes this can happen,’ Mourinho told MUTV.
‘The reality is that the ones on the pitch were the ones who were not in the last match, and probably the ones who are not going to be in the next match.
‘I think they lost a good opportunity to play in a semi final, to have two more matches to play, but I don’t want to blame the players at all.
‘I think they were professional, it was not a case of we don’t care about the game, we don’t have responsibility, we don’t have pride, they showed that after the 1-0, they showed that until they scored the second goal in the last second and we had no chance to react.’
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