I may be interpreting wrong, so here's how you do it:
1. go to the battle tower
2. deposit your pokemon into a (preferably) empty box. It is possible to overwrite your pokemon, so don't say I didn't warn you.
3. save your game.
4. go back and withdraw your pokemon that you want to clone.
5. talk to the receptionist on the far right. when she asks you to save your game say yes
WARNING: DO NOT turn off your game during the pause in between! Doing so may corrupt your game so that you'll have to start over!
6. When you are asked to save your game, say no. After she says "we hope to see you again", turn your game off (DO NOT SAVE)
7. Turn your game back on, and check to see that you're still in front of the receptionist. If you are, you have successfully executed (no pun intended) the cloning glitch! Here is a recap of the warnings:
DO NOT turn off your game during the pause.
DO NOT attempt to clone a full party in one run. Doing so may replace an existing pokemon with the clone. Look for empty space!
You can also find this online.