Cristiano Ronaldo sent the Red Devils 1-0 ahead in the 13th minute of the contest, but Ole Gunnar Solskjaer's side struggled after Aaron Wan-Bissaka was shown a straight red card in the 35th minute.
Young Boys levelled the scores in the 66th minute through Moumi Ngamaleu before Theoson-Jordan Siebatcheu scored the winner in the 95th minute, and Merson has said that Man United 'have not got going' this season despite picking up some impressive domestic results thus far.
"Manchester United haven't got going. Against Wolves, they were very fortunate. Against Newcastle when it was 1-1, it was a heads-or-tails game. It could have easily gone Newcastle's way," Merson told Sky Sports News.
"Champions League football is hard and it doesn't matter who you are playing. For Young Boys, this is their biggest game ever. And if you don't match that, you are in trouble. This isn't the biggest shock to me."
Man United will return to Champions League Group F action at home to Villarreal on September 29.
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