Suffocation Trap Causes Clipping

I used a design I found on youtube for a mob grinder that includes a suffocation trap (https://www.youtube.com/watch?v=IKM3-DaB9vA). The entities(zombies) do indeed suffocate, but also clip out of the trap and fall into the void. (Image shows the clipping)

How to recreate:
1) Build the grinder
2) Wait for the mobs to spawn
3) When the suffocation part activates, entities should clip into the surrounding blocks.