Player head collision box activated while jumping into block that is too high

Sethbling describes what I'm talking about very well:
Oneway Doors

The yellow box as described in the video activates while in the air of a jump and clips the bottom edge of a block sometimes and the player looses momentum.

Steps to reproduce
Dig out a 4 block tall tunnel of any length.
Now place random blocks on the 4th layer.
Sprint and jump down the length of the tunnel.
Occasionally the player will clip the bottom of the block and loose momentum.