This debug mod was created a few snapshot ago, and since there is no updates in this world, and the world regenerate when the version change to generate new blocks states, previous TileEntity were not delete and new one are not created(if they are supposed to be created)
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This is exactly what I do, the command I made are just to see what TileEntity are in the block below me, otherwise I didn't use any command to modify block/TileEntity in this world. I just create this world, and open it in different snapshot.
Then I don't see the relation between my issue, and MC-58898

I use gamemode 1 to easily see what TileEntity is in the block below me(gravity help), but this bug can be reproduced like this :
Create a new debug mode world in 14w29b, wait few second in order to generate then save and quit.
Open this world on the 14w31c snapshot and check flower pot, and you may see some chest inside some flower pot(and skulls too).
Commands I made just show that some block have wrong TileEntity.
This is one of the way to reproduce this bug, it may also work by switching from an older snapshot to the current one, and it may also happen by switching from the current one to a future one.

See it.