The Portuguese has suggested that events late in the game were out of his side's control, firing shots at the officials in particular
United now sit six points behind early Premier League leaders Manchester City, and Mourinho has lost three consecutive competitive games in a single season for the first time since he was in charge of Porto in 2001-02.
The frustrated Portuguese felt Anthony Martial had been fouled in the build-up to Watford's first goal from Capoue and suggested his side were on top when Watford struck twice in the latter stages.
He told BT Sport: "In the first half for about 25 to 30 minutes we didn't play well and that is something that we can control. We can improve, we can work on it.
"Then the referee and the linesman's mistake is not under my control. I can't do anything to improve it. That [the Martial incident] is an obvious situation.
"I think there is no debate, no controversy. I think that is an obvious situation, like it was obvious last week against Man City but it's something I don't control and I cannot even be critical of.
"In the eyes of everyone - it doesn't matter whether you are a Manchester United fan or a Watford fan or whatever - it was obvious.
"In the second half we were much better. We get the draw [equaliser] and after that we were the team. Gomes makes a phenomenal save and the lucky moments again are not something we can control.
"We cannot control the referee, we cannot control the lucky moments. We had that period where, in the stadium, everyone was thinking about Manchester United going on to score a goal and win the game.
"The only thing we can control is our individual and collective mistakes like for their second goal."
Mourinho went on to describe the decision not to award a foul on Martial following Miguel Britos' challenge as "ridiculous" and reiterated his belief that factors outside of his control played a key part in the loss.
He said to BBC Sport: "The first factor depends on ourselves, it relates to our individual mistakes and collective mistakes as individual players and as a team. We have to improve something, it is in our hands.
"The second factor is the referee and I can't control their mistakes. The story of the game is the result and not the ridiculous situation of the first goal.
"The third factor is luck, we didn't have it. We were the best team when we lost."
He addded: "We started the season very well and had good results. I feel the first moment we had a defeat, a difficult situation, some of the boys are having a bit of difficulty coping with the negativity.
"You see Ashley Young, his mentality, the happiness and confidence he brought to the game is something more players need to have."