United were lucky to head into the break level with Bournemouth missing several chances to put the game to bed.
Martial scored 10 minutes before half-time to cancel out Wilson’s early strike, before Rashford’s late strike won it for United.
The win pushes the Red Devils closer to the top four but Mourinho wasn’t impressed by the whole performance.
“Defensively awful. Absolutely awful,” Mourinho told BT Sports after the game.
“And when I say defensively I don’t just mean my defenders, I mean as a team.
“At half time I thought I was the luckiest manager in the Premier League. Because to be 1-1 in a half where it should be like 5-2 or 6-2, we were really lucky because we were really poor.
“We didn’t press. The work we did during the week – I feel like people watching this game won’t believe how hard we trained this week.
“The first half was a disaster. Then in the second half it was exactly the opposite. We created a lot of chances, we pressed higher, we had much more aggression, intensity, intention.
“We deserved to score before ninety-somethingth minute.”
“[I had] Strong words [at half time] but I was calm. I started by being positive, saying it was impossible to play worse, so the second half was going to be better for sure and obviously it was.
“We performed much better as a team. I can’t understand.
“My assistant came to me and said we had the best warm-up of the season. Everyone was very focused, great intensity. It was also a phenomenal week of [pre-match] work.
“I can’t believe how badly we started.”
Mourinho’s men next play Juventus in the Champions League on Wednesday.