Yeah, I'm not the biggest fan of the anime but I can at least see what they were going with the Master Ball fail. Humor, folks. "Why not have the Master Ball fail on an ordinary Pokemon in the stupidest way possible? LAUGH DAMN IT." Still doesn't mean it's good.
If the anime doesn't introduce a good Master Ball that catches things, I'M GOING TO RIP THE WRITER'S THROATS OUT.
The Master Ball cannot fail against a wild Pokémon, unless the game specifically forces it to (Pokémon Tower literal ghosts and Marowak, Kyurem under Ghetsis's control). Any "Master Ball has a 1/65536 chance of missing" rumour is a pile of steaming bullshit, because it simply doesn't work like that; the game skips the formula entirely when you use one of the things. (And no, it never had a ×255 multiplier either)
Meanwhile, at the writers office. I think we should do a thing with the masterball and the thrill of that one moment when you really needed to catch a Pokemon, and you decided to use the rarest item in the game. So this one guy uses the Pokeball and he finally gets to catch this Pokemon he's been chasing his whole li- NOPE NOPE sorry Ted, but we gotta do a joke about the rarest thing in the game not doing what it's supposed to because we want them to be all like facepalm so we gotta have it be eaten by a whiscash ok team you got that? EPISODE IS GO FOR RELEASE!
back in gen 1 mewtwo dodged my fucking master ball for those that never played red blue green or yellow, if a pokemon's speed was higher enough than the pokemon u had in battle it could dodge the balls, also legendaries could do it anyway being legendaries