Eric Maxim Choupo-Moting's brace for Stoke cancelled out goals from Marcus Rashford and Romelu Lukaku for United, who still remain top of the table after matchday four.
Mourinho felt his side deserved more than a point against Stoke
The result brought an end to United's 100 percent record in the Premier League and despite many feeling a draw isn't a bad result away at Stoke, Mourinho feels his side deserved all three points.
Speaking at his post-match press conference, Mourinho said "it was a difficult match for different reasons".
He added the international break meant "my players are not the same" and they "weren't performing at their normal level".
The United boss went on to say that Stoke "fought hard" for the point and they got it but he felt that his team's "performance was more than enough for the point".
Mourinho felt his side had done "enough for three points" given the amount of the ball the team had.
Mourinho 'very happy' with the character of his players to come from behind against Stoke to get a point
One thing that Mourinho was happy with was the character of his players in the game despite the heavy workload that most of them had during the international break.
Mourinho said "it's not easy to come from behind" at Stoke on a normal day.
He added that given "the handicap of the players' condition" before the game "I'm not disappointed" with the result as they gave their all for the team to try and come away with yet another three points but it wasn't to be.
Mourinho will now have to go away and prepare his side for their opening UEFA Champions League group stage match against FC Basel on Tuesday evening at Old Trafford with a win the order of the day to start their campaign.