Title. This only happens when firing a projectile upwards (negative yaw/aiming 'above the horizon'), the higher the player aims the further the projectile will clip into the ground when bouncing (about 1-2 blocks max). The projectiles will continue to clip on consecutive bounces, projectiles fired with positive yaw (downward) will not do this, even on consecutive bounces This seems to be a client side only issue

after some further investigation, it seems that the vertical bounce/impact height of the projectile is directly proportional to the yaw of the player. Launching the projectile with negative yaw will cause it to clip into the ground, while launching the projectile downward causes the projectile to bounce/impact before it can reach the ground

This issue has been fixed in 1.14