Thanks so much for checking out the game!
What might be happening is this: When you move up or down, the hull of the submarine rotates a few degrees. That also rotates the hitbox. This is intended to conform more closely to the silhouette of the visible sprite, but it may be counterintuitive at times. For example, if you are hiding in the seaweed and an enemy is sliding past above you, pressing down may get you clipped, because the sub will raise its tail.