Pokedex has never been an issue when used it. shedinja's a wierd 'mon though. you can't catch one, maybe you had something like "egg hatched" on the description of were you found it, which is of course impossible and the game got confused. i get the blue line thing when i put awkward stuff in those boxes, but an egg is a new one. Try again with a different input if you want.
or your game is haunted by the ghost of egg shedinja. if that's the case write a creepypasta immediately.