It's extremely rare, but there's a reason this is possible. Smash may be a 2D game, but the characters' hitboxes are affixed to their models, which still operate in 3D space, so there are times where things look like they should collide (and indeed would if everything was flattened along the Z-axis like a sprite-based game) but just miss each other; usually the results are much more minor than this, however.

Shulk must've posed in exactly the right way for the shot to physically pass him in 3D space.

The future is ours to decide! I've decided your attack will miss!