Goals from Belgian duo Marouane Fellaini and Romelu Lukaku put the Red Devils in control over their Swiss visitors at Old Trafford, before Marcus Rashford marked his Champions League debut with the third goal late on.
Mourinho was unhappy with how his side's playing style changed after they had gone two goals ahead, though, claiming that complacency may have crept into their game.
"Three points are important at home. Until 2-0 we were very stable, we played with confidence. After 2-0 everything changed, we stopped playing seriously and stopped making right decisions. We could have put ourselves in trouble," he told BT Sport.
"We were playing fantasy football, PlayStation football. I don't like it, flicks and tricks. We gambled and you have to respect your opponent. I don't know if goal difference will play a part. We lost position, our shape, we lost balls in easy situations. I didn't like it, the players relaxed too much.
"I keep saying the same about Fellaini. He is a player with special qualities and he gives me multiple areas of action. He is one of my most important players."
The result, which was the club's first Champions League win since November 2015, lifts United to the top of Group A after matchday one.