The block breaking particles are drawn behind the block selection box, like you can see in the screenshot down below!
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This also applies to particles and water, they're drawn behind the water, regardless of where the water actually is.
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.
Confirmed.
Applies also to survival mode.