This has been happening for the past 2-3 weeks.
Whenever I try to put my main snorlax into 6th slots, it always says, "You don't have a pokemon in that slot!"
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However, I fix this by logging out and logging back in.
But when I log out, it usually moves the normal snorlax into the 5th slot and removes the shinysnorlax.

Have you tried sending them all to your box and then redoing your team? That sometimes has happened to me, but that's seemed to work.

My pokemon are just cloned sometimes :L It usually happens when a text says "You've selected an Invalid pokemon" yet it's still in the party and if you go to your box and look for the pokemon, You can have both the Clone, as well as the main one on your team. this has yet to happen to me though

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Okay the bug is starting to take affect to me :L