Witherproof Glass not keeping the Wither in?

[darkspyro92]

So I made a box of Witherproof glass, and after self-destructing, the Wither rose out of the box of glass. How in the world does that happen? His self destruct destroyed a small amount of area outside the box as well. I checked and there are no holes in the box besides the one when he destroyed the vacuum hopper.

[James103]

If anyone else runs into this in the future, make sure the box of Witherproof blocks has at least 4 blocks of vertical clearance inside instead of 3. 3 blocks is enough for the spawning structure, but the hitbox of the Wither itself is 4 blocks tall.

#####
#...#
#...#
#...#
#...#
#####

where # is a witherproof block and . is air.

Furthermore, make sure all the corners and edges of the box are filled in, not just the faces, otherwise the resulting explosion can damage blocks outside the box.