Cristiano Ronaldo sent the Red Devils ahead in the early stages of the match, but the contest turned when Wan-Bissaka received a straight red card for a late challenge on Christopher Martins.
Maguire admitted that he 'could not really comment' on the challenge but appeared to suggest that his teammate did not deserve to be sent off in the European contest.
"I can't really comment because I haven't seen it back. I'm sure in slow motion every tackle you can make something for it. Any tackle that's a foul you can say they go over the ball, but I can't really comment," journalist Mark Critchley quotes the Man United captain as saying.
Moumi Ngamaleu levelled the scores for Young Boys in the 66th minute before Theoson-Jordan Siebatcheu scored the winner for the home side in second-half stoppage time.
Man United have now been beaten in seven of their 11 Champions League matches since Ole Gunnar Solskjaer's arrival as head coach.