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.
CSKA Moscow 
FC Rostov 
Leicester 
Chelsea 
Valencia 
Betis 
Dynamo Kyiv 
Chornomorets Odesa 
Verona 
Inter 
Bayer Leverkusen 
FC Heidenheim 
Borussia Dortmund 
SC Freiburg 
VFL Wolfsburg 
Union Berlin 
Arsenal 
Nottingham Forest 
Everton 
Brentford 
Spartak Moscow 
Lokomotiv Moscow 
Rangers 
Dundee Utd 
Atletico Madrid 
Alaves 
Lens 
Marseille 
Ingulets Petrove 
Shakhtar Donetsk 
AC Milan 
Juventus 
ST Malo 
Bordeaux 
Manchester City 
Tottenham 
Eintracht Frankfurt 
Werder Bremen 
Girona 
Espanyol 
Feyenoord 
Heerenveen 
ST Etienne 
Montpellier 
Grenoble Foot 38 
Heart Of Midlothian 
Celtic 
Reims 
Lyon 
PSV 
Groningen 
Celta Vigo 
Barcelona 
Benfica 
Estrela Da Amadora 
Sparta Rotterdam 
AZ Alkmaar 
Southampton 
Liverpool