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Justin Bieber was straight up BOOED at the Billboard Music Awards last night ... and not like 1 or 2 people ... it was a straight up CHORUS of boos ... and it made Justin super uncomfortable.

It all went down when Cee Lo called on Bieber to receive the first ever Milestone Award -- but when Bieb got to the stage, the crowd turned on him.

Of course, there were some screams from the hardcore Bieber fans ... and JB managed to silence the haters for a minute by thanking Jesus Christ (who's gonna boo JC?) ... but overall, more boos than a haunted house.

As for the Bieber/Selena Gomez situation, the two were NOT seated together during the show -- despite a pre-show photo of the seating arrangement that suggested they would be.