The Blues manager appeared somewhat stunned after watching his Blues team go down to a late Oussama Assaidi goal at the Britannia Stadium.
Andre Schurrle had given the visitors the lead in the Premier League encounter but goals from Peter Crouch and Stephen Ireland put Stoke in front before Schurrle made the scoreline level once more.
However, Assaidi's intervention meant the points stayed in the Potteries.
"I don't feel very comfortable to tell you exactly what I think about the game," Mourinho told Sky Sports soon after the final whistle.
"I prefer to be simple and pragmatic and say that we scored one goal less than them and we lost.
"I can't analyse with you certain aspects of the game, or individual performances.
"I don't want to take credit away from them. If I was Mark (Hughes), I'd be upset if the opposition manager just said 'we lost'. They did something to get a point... maybe not to win."
Mourinho was asked about his defence, having conceded six goals in back-to-back away games at Sunderland and Stoke.
"It's a big concern," said the Chelsea boss. "I don't organise my teams this way. Individual mistakes sometimes kill a team, and the way we work.
"But, there are also the goals we didn't score. In the first half, we had lots of occasions in which a simple movement and finish would have meant the job was done. We should score more goals than we did.
"Our first half was fantastic. There was a great quality of football, and we dominated. We had dozens of situations when we won the ball back... but we didn't kill the game.
"By conceding late in the first half, we gave life to an opponent who was in big trouble. In the second half, they had more life. It was less of football - free-kick, yellow card, push here, pull there - and it was more difficult to play."
Having now dropped to third in the table, behind Liverpool on goal difference, Mourinho added: "I am not looking at opponents directly. I am looking to my team, and my performance.
"The big problem for me is the way we play. The other day at Sunderland, we conceded goals at set pieces and today we had another one - but don't speak to me about organisation, because it's not about that.
"We don't score enough goals for the football we play."
When asked what the differences were between his previous Chelsea team and the current squad, he said: "A few! A few very important differences.
"But I have to try and get the best out of the squad I have. I see a big evolution in some players - pressing high, recovering balls, playing fast, mobility in the three players behind the striker. In my opinion, we are playing some very good football... and we concede some goals that we shouldn't."