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Problems with "Super Cell Builder"

I’m new to Avogadro. I used a .cif file from the literature to generate a unit cell of a small molecule and then replicated it using “Super Cell Builder”. There are at least two problems. 1. The Cartesian coordinates don’t seem organized by molecule. How can I do this? 2. One of the atoms is on top of another atom in the cell when I replicate the unit cell using “Super Cell Builder”. How can I avoid this? Thanks in advance.