Nothing to worry about, AFIK it doesn't really delete any extra files.
But as to why it exactly happens I haven't found out yet.
You have some external volumes mounted as well, correct?
In my system, every mounted volume seems to contribute a minimum of two items that get deleted by Secure Empty Trash, even if there is just a single item in the dock Trash window beforehand. Making hidden files visible in Finder does not show any additional items in the various Trash folders before the secure delete.
I currently have a total of 16 partitions mounted. If I first Secure Empty the Trash, then put a single item into the Trash from my Desktop and then Secure Empty the Trash again, I will see a progress window saying that 34 items are being deleted. Reducing the number of mounted volumes reduces the count by two for each volume that is unmounted.
I don't know what the extra items actually represent. They may be part of the always-hidden directory structure that exists in every hfs+ volume.