The block breaking particles are drawn behind the block selection box, like you can see in the screenshot down below!
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Confirmed.
Applies also to survival mode.

This also applies to particles and water, they're drawn behind the water, regardless of where the water actually is.

Also behind clouds.

This appears to only happen on some blocks. In 13w09b, I have observed it on wood and stone, but NOT on crafting tables or furnaces.

Resolving as a duplicate of MC-9553 because I am fairly certain that these stem from the same issue.