In "Pokémon Paparazzi" Team Rocket has successfully captured Pikachu and defeated Ash and Todd. You'd Expect: Them to the get the heck out of there. Instead: They throw bombs at Ash and Todd and are fooled into posing for a shot, where the bombs blow up in their hands, thus defeating them.
In several episodes, Team Rocket has Pikachu, has eluded Ash & co., and is making their getaway. You'd Expect: Escaping in something more inconspicuous, such as disguising themselves and driving away in a Jeep once they were out of sight. Instead: They slowly float away in a distinctive Meowth-shaped hot air balloon, leaving themselves visible and vulnerable to Ash's Flying-type in that region.
In another episode, Ash is fighting Misty in the Whirl Islands Tournament. When Misty tries to use her last Pokémon, Psyduck comes out. Ash has his Kingler out on the field. However, Psyduck has a tendency to go into a Psycho rage when it gets a headache. Ash knows this; he has seen it on numerous occasions. You'd Expect: Ash to command Kingler to tickle Psyduck, or better yet, nudge it into the water. Instead: Ash commands Kingler to use Vicegrip. On Psyduck's head. A few seconds later, Ash's face comes in contact with flying crab.
Ash's general stupidity in regards to Team Rocket. You'd Expect: Ash, over his many encounters with Team Rocket, to smart up and realize that their weapons/tools/whatever are more often than not designed to nullify electric attacks. Instead: Time and again, Ash sics Pikachu's Thunderbolt on their asses as a first attack, with unsuccessful results.
On a similar note... You'd Expect: Ash and his company to recognize Jessie and James's hair colors, styles, and voices after all the constant encounters, and learn to identify them through such. Instead: They fall for the disguises almost every time.
Team Rocket's obsession with saying their motto Once an Episode even when it would screw up their plans such when they're supposed to be incognito. You'd Expect: Team Rocket to realize that this time they should keep their mouths shut and continue with executing their plan. Instead: They say their motto as usual, either blowing their cover and/or leaving themselves open to attack, ruining a plan that would otherwise have gone off without a hitch.
At the end of the eighth movie, Lucario needs to use his Aura power to heal the World Tree, but the amount of Aura required would be fatal to him. You'd Expect: Lucario to ask Ash, who has recently been revealed to have Aura power, to help him heal the tree, thus preventing a senseless loss of life. Instead: Lucario does it himself and dies a tragic, pointless death.
Barry is battling Ash. Ash's Chimchar defeats Barry's Staraptor. You'd Expect: Barry to send out his Empoleon, taking advantage of Elemental Rock-Paper-Scissorsand the fact that Empoleon is a fully evolved Pokémon with powerful attacks, unlike Chimchar. Instead: He sends out his Roserade, giving Ash an Elemental Rock-Paper-Scissors advantage.
Another one with Barry is when he has his Hitmonlee out against Paul's Ursaring. You'd Expect: That Barry would have Hitmonlee use Fighting-type attacks, which are strong against Ursaring. And no, this isn't a case of this only being true in games and not in the anime. Barry outright states that this the case; it's the entire reason he sent out Hitmonlee in the first place. Instead: Partway into the fight, Barry arbitrarily decides to have Hitmonlee start using the Fire-type Blaze Kick for no apparent reason. This ends up inflicting a burn on the Ursaring, which causes its Guts ability to kick in, resulting in Hitmonlee getting pulverized. Sure, Barry's a bit scatterbrained, but he's not this stupid.
Most characters' stupidity when it comes to the type chart and how the different types match up. You'd expect: One battler to send out a Pokemon with a type advantage or a resistance to the opponent's moves. Instead: They usually send out one with a disadvantage (and sometimes even a 4x weakness) and get curb stomped (Such as Cameron sending out a Ferrothorn, a steel/grass type, against Ash's Pignite, a fire/fighting type, or sending out Swanna, a water/flying type, against his Pikachu, an electric type. All in one battle, too. He could have easily switched the order and sent out Swanna for Pignite, and Ferrothorn for Pikachu.)
Ash's final battle with Iris in one of the Club Tournaments, You'd Expect: Ash would know Iris saved her Excadrill for the final battle, so he'd use Palpitoad. Instead: Ash sends out Pikachu, who's two most powerful attacks (Thunderbolt and Electro Ball) have no effect on Excadrill AND Excadrill resists his other moves (Iron Tail and Quick Attack).
Stephan wins a tournament to make a wish that is guaranteed to come true You'd Expect: He'd wish to win the Pokemon League which is the biggest tournament in Pokemon Instead: He wishes to win an upcoming tournament that has nothing to do with the Pokemon League
In "Candid Camerupt" The Group is having a friendly battle with a family. Max is up and he's up against a girl he has a crush on and is borrowing one of Ash's Pokemon and wants to go easy on her. You'd Expect: He'd pick one of the calmer docile ones he has who'll listen to him. Instead: He picks Corphish. Said Pokemon doesn't listen and beats up her Marill causing The Girl to hate him and ruining any chance he had with her.
In "Friend And Faux Alike", Team Rocket has a mecha-Heliolisk that they gleefully proclaim can repel electric attacks. You'd Expect: Ash to order Pikachu to use Iron Tail or Quick Attack, or for him to use one of his other Pokemon. Instead: He calls for Thunderbolt, which gets absorbed. You'd Expect: Ash to learn from this and use a non-electric attack. Instead: He calls for Electroball, with the predictable outcome.
Mewtwo, having been persuaded to work with Giovanni, is still wondering what his purpose is. You'd Expect: Giovanni would keep in mind Mewtwo is one of the strongest Pokémon ever, and can take down multiple opponents all at once, AND that prior to this, he destroyed an entire laboratory and all those inside in a fit of rage over the scientists not caring about him, just what he is. Thus he should be careful not to offend/anger Mewtwo. Instead: He tells Mewtwo that, as Mewtwo was created by humans, his purpose is to serve them and not question it. Mewtwo promptly causes an explosion and takes off. But wait, there's more! It was this moment that convinced Mewtwo that humans cannot be trusted and nearly leads him to cause The End of the World as We Know It. Way to go, numbnut.
The villain Gelarden has just captured Moltres and Ash & co accidentally. You'd Expect: The villain to keep Ash and friends imprisoned, or just for kicks, dump them into the sea. Instead:He lets them go as he monologues. A few minutes later, his flying base is in ruins and the two birds he captured have escaped. Nice work, moron.
Scraggy is accidentally left behind on a train station...and the train is leaving You'd Expect: Ash to just recall Scraggy and send him out again. Instead: Ash tries to get Scraggy to jump onto the moving train. Scraggy fails, and has to be caught by Snivy's vines.
Jasmine is traveling through Ecruteak City when there's an earthquake. You'd Expect: She run somewhere she won't get crushed. Instead: She runs to what has to be the most structurally weak building in the area: A crumbling, 700-year-old wooden tower! Not just inside it, either, but to the top!
Ark uses a bound-and-gagged Flannery as a hostage to lure Sapphire into an airtight cable car, which he locks and then floods with his Azumarill—but not before knocking out Toro and putting an air bubble around his head to make certain he can breathe in the flooded car. You'd Expect: Ark to let the water do the work. He can breathe; they can't. The entire situation, at that point, was engineered so he couldn't hope to lose. Instead: not only does he summon a Sharpedo to expedite the killing, but even after its teeth are broken off, he flagrantly violates Rule 6 of the Evil Overlord List, with some of the gloating going straight into Tempting Fate. Yes, Sapphire can hold her breath that long, and she does, up to the point she manages to cut a hole in the glass with the same teeth she just broke off!