In the end of "Hypno's Naptime" Misty slips her pokeball out of her bag and it touches Psyduck who was behind her. Since Psyduck is so weak it easily got in. Then Misty complained about how she got such a weak pokemon. Then it showed Psyduck going "Psy-yi-yi!" in a gray background in a circle. This wasn't supposed to show what's inside a pokeball, it was just to finish off Misty's complaining by showing us how stupid Psyduck is and how hard it's going to be for Misty! It wasn't important, just to finish off the episode.
Heheh I got it on tape so I saw it over and over and over!
I have always thought, that when a pokemon goes into a pokeball, it doesn't become a pokemon anymore. Notice that when a pokemon comes out of it's pokeball it's a light substance....maybe they're like that in a pokeball? That would prove why Psyduck and Pikachu and Wobofett don't like it in there; they're not actually 'Pokemon' while in a pokeball!