Overlapping fullback is completely free in the box and drills a cross at high speed, Pique can't really do much.
He messed up here, the two Barca players went to close the cross and Pique should have kept awareness of Mueller. But, this also shows he doesn't trust the rest of the team(they often fail to track opposition players) so he was drawn towards the centre of the goal which is where the more immediate danger was.
There's 3 Bayern players by the near post and only 2 Barca players(Pique, Bartra). He's also correctly played Gomez offside. Can't really blame him for this either.
Seriously, Pique was immense in the game. With the amount of pressure he was under and the risks he had to take and the number of attacks he had to repel of course there would be instances where he falls a fraction short. Barca would probably have been 3 or 4 goals down at half time if not for him. He also tried to help the stalling Barca attack, his surges forward made progress. If he left space behind then other players(notably Busquets) should cover for him.