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Burning arrows can't ignite tnt when they hit it at the top

Mushroom Block gives Brown Mushroom with PickBlock Key

Punching a bed block doesn't show cracks on the top

Hoppers display a breaking animation on their top

Lava can't be seen through ice

Furnaces won't work

Log top textures messed up

Double extending pistons act differently at different Y values. (As far as I can tell)

Water

Fence-gates with pressure-plates on top only open from the side and not the top