Steps for replication:

Place a block (any kind you can easily break for the demonstration)
Place a flower pot on the block.
Put dirt in the flower pot and some kind of plant.
Apply a block (I used a BOP dead wood) to the pot as a cover.
Break the block under the flower pot - this causes the pot to drop, along with the dirt, plant, and TWO copies of the cover block.

What version are you using? The most recent builds addressed a dupe bug similar to this one, and I'm not able to reproduce the bug.

I was using the last public release from the forum thread. I'll pull down and build this weekend, and get back to you.

I confirm this issue is fixed in the latest source (checked out as of 15 minutes ago)