When using the /setblock command with air and relative coordinates the block cannot be place unlike it can with standard coordinates.
Broken Relative Command
/setblock ~ ~2 ~ minecraft:airWorking Standard Command
/setblock 0 2 0 minecraft:airComments 2
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Is this still a concern in the latest Minecraft version 13w48b? If so, please update the affected versions in order to best aid Mojang ensuring bugs are still valid in the latest releases/pre-releases.