Box change glitch
1) Load your boxes via "Move Pokémon"
2) Select a Pokémon but don't do anything
3) While the Pokémon is still selected change boxes by touching the box name, selecting "Switch Box" and then going to another box.
4) Go back to the original box and the Pokémon may "disappear". This doesn't always work, so you may need to try more than once.
Even though the Pokémon has disappeared, it's still there and you can select it. It will be highlighted in red and its silhouette is based on what Pokémon was in the same spot in the last box you switched to, otherwise the original Pokémon if you viewed no Pokémon at all after the box switch and returning to the original box.
If you put this Pokémon in the party with "Party PkMn" it may look like you're putting an empty space in the party. Open the party again with Party PkMn and the Pokémon will be given a visible mini-sprite, which may even be wrong.
Example of a wrong mini-sprite
With Sableye in position 1, switch to box 4 with an Elgyem also in position 1. The end result when putting the invisible Sableye in the party is a Sableye with Elgyem's mini-sprite.
You can give a Pokémon the mini sprite of an Egg, or an Egg the mini-sprite of a Pokémon, but you can't release an Egg/view the hatched Pokémon's stats that way.