This has happened to me 3 times now! The first time I did it, I got 2 of the same baby. When I deleted that baby's character, I got Mom acting as the baby the next time I went in the game. Then I created a new neighborhood, new characters, went in SimPe to change skills and increase their money then boom! I got two toddlers again, same character number, I even got the message saying something like "duplicate characters found, may cause error in game play". I started new neighborhood again, made new sims and went back to SimPE. This time I got 2 of the same young adult.
I couldn't move in the family with duplicate sims, by the way. Game just freezes while it's loading family data.
What is going on? This has never happened with the older version before. Anyone else with this problem?

Which Version do you use?
I did quite some test with the procedure you described, yet I was unable to get a cloned Sim.

I have version 0.44.2046.26185. I wish I could remember exactly which steps I took or which attributes I changed. I do remember one of those times was when I tried to change Dad then he disappeared from the Sim Browser list and his son was listed twice.
I was trying to change their last names, skills, and family money. Could it be because those characters were just moved from CAS into family bin and not even moved into a house yet?
The first time it happened, though, was with an established family. I had deleted Dad's (another family) custom skin tone because his daughter had the weird baby face (with the eyes on the forehead, etc.) and someone suggested it was because of custom skin tones. When I tried to enter that family, game froze. That's when I went to SimPe and found two of the same baby! To think that I wanted to get rid of her only to find two of her! :cry:
Anyway, I haven't used SimPe since. I've finally got a new neighborhood up and running and I'm afraid to mess it up again.