Begley, who was by coached by Danny O'Donoghue, beat fellow finalists Mike Ward, Leah McFall and Matt Henry on Saturday's (June 22) final.
A source present at the final told Digital Spy that will.i.am "walked off stage from his chair looking really cheesed off and shaking his head" after Begley's win was announced.
When cameras later cut to the coaches after Holly Willoughby interviewed Begley about her victory, only Jessie J and Tom Jones were shown in their chairs, with O'Donoghue already on stage.
The Black Eyed Peas singer later reappeared on stage with the other coaches halfway through Begley's performance of 'My Immortal', after allegedly being told to return after consoling his act McFall.
Earlier this month, will.i.am revealed his fears that The Voice UK would not succeed without a superstar winner.
He has also suggested that he is unsure about a return for series three of the show.
Watch Andrea Begley perform 'My Immortal' below: