Why do some Pokemon vanish in Pokemon Pearl?

Answer 1

if you mean vanish as in flee like mesprit, cresselia, moltres zapdos and articuno, its because they are supposed to do that and they do that in platinum and diamond too. you can only get moltres zapdos and articuno in platinum. to stop them from fleeing, you should have masterballs or a TRAPINCH in your first slot but you cant switch out because it knows sand trap or whatever its called to stop Pokemon from fleeing or have a haunter or any ghost Pokemon that knows mean look or a sudowoodo that knows block and USE those moves IMMEDIATELY when you see them. hope i helped! :)