I had moved my Infernape to slot one, moving my Rhyperior to slot 3, and somewhere between my Infernape became two and filled my second slot as well. In the end i have two infernapes and one of my pokemon, a Scpetile, is missing. I looked at my public profile, and it displays the correct team, though when i go into a battle I still have the duplicated Infernapes. I viewed all my pokemon and it also had the correct number of Infernapes and a Scpetile. I am unable to transfer the Scpetile from my box, for it says it is still in my team. I am concerned that this will be abused and/or cause any other damage to players accounts.
Edit* I would also like to bring to focus that when ever I logout, the pokemon in my sixth slot is returned to my box, I will have to pay more attention and see if anything else triggers this auto boxing

all you have to do is go to your pokemon and then click the here button [you must login to view links] and will move all the pokemon, then log out to make sure then log back in and put your pokemon back up :) hope it helped

Yes, thank you so much! I wish i would of realized my self, sense it was so simple