You'd Expect: That they'd follow him down the pipe back to his castle and teach him a lesson.
Instead: They let him get away. In one episode, they are even shown standing on one (granted, that was an animation goof but still).
Adventures of Super Mario Bros. 3
"Reptiles in the Rose Garden": Mario and friends see Bowser's Doomship hovering overhead.
You'd Expect: That they'd just make a run for it.
Instead: They stand motionless, somehow avoiding getting shot by the ship's gunshots, and as a result, get captured by the Chain Chomps that King Koopa sends down after them. They can't even warn the USA that the Koopas are coming.
"Never Koop a Koopa": Koopa announces that he and the Koopa Kids are admitting defeat and moving out of the Mushroom Kingdom. He hands Princess Toadstool the key to his castle as a token of forgiveness. After he disappears, Luigi tells her that she's being set up and to dispose of the key.
You'd Expect: Princess to trust Luigi and determine that all this is indeed too good to be true.
Instead: She talks the Mario Bros. and Toad into visiting the castle with the key in her possession, thinking she can turn Castle Koopa into a retirement home.
"Toddler Terrors of Time Travel": King Koopa and Kooky plan to trap the Mario Bros. in Brooklyn by blocking the only way they can escape, a woman's drainpipe that leads to the Mushroom Kingdom. They don plumber outfits and introduce themselves to the lady.
You'd Expect: That she'd see through their paper thin disguises and call someone else to fix her plumbing or, better yet, alert the police.
Instead: She believes them to be real plumbers and invites them into her home. There, she reveals a problem with the same bathtub drain that brought them there. King Koopa and Kooky proceed to clog it with anything they can find.
To Be Fair: Mario did say she was "a bit daft," and Koopa and Kooky pretended to be costumed plumbers.
"Oh, Brother!": Mario and Luigi have a heated argument, with the latter threatening to walk out of Toad's House where a thunderstorm (created by Kooky) is brewing.
You'd Expect: Luigi to realize that going outside in the middle of a thunderstorm isn't the safest thing to do and maybe try to patch things up with Mario.
Or: For Luigi take a Frog Suit at Princess Toadstool's request since it had been raining nonstop for two weeks by this time.
Instead: Luigi storms out of the house without a Frog Suit, claiming he doesn't need one. Mario then goes after him without a Frog Suit as well.
Super Mario World
"Fire Sale": Mario, Luigi, Peach and Yoshi have cornered Kootie Pie inside Ice Palace which is beginning to melt due to Mama Fireplant's tirades. Mario, Luigi and Peach have all been frozen by Porcupine Fish, leaving Kootie Pie to deal with Yoshi.
You'd Expect: That Kootie Pie would simply stay put and perhaps taunt Yoshi in hopes that he will also step on a Porcupine Fish if he chooses to run toward her. In addition, Yoshi is afraid of water so he may panic and accidentally touch one.
Instead: Kootie Pie goes after Yoshi and steps on a Porcupine Fish, enabling him to rescue Mama Fireplant and his friends before the Ice Palace collapses.
The Result: Kootie Pie becomes frozen from the shoulders down in a block of ice. Her screams are unanswered because her Koopa Troopa minion refuses to help her.
"Send in the Clown": Luigi, after seeing a poster for Koopaling Bros. Circus, tells Mario, Yoshi and Peach that King Koopa may be luring the cave people into a trap. They take a Star Path to Neon Castle and find the circus tent.
You'd Expect: For them to round up the cave people and leave immediately.
Instead: Mario persuades the gang to watch the show together with the cave people. The heroes don't discover they're in trouble until a nose falls off one of the Rex's clown disguises due to a pie fight gone awry.
"Ghosts 'R' Us": The Mario Bros. and Princess have been caught by Wizardheimer in the Enchanted Forest. He threatens to blow them up with a Bob-omb if they don't go in a warp pipe leading to his haunted house.
You'd Expect: For them to just run like the dickens since they're in a huge forest.
Then: For their science fair project, Hip and Hop build a volcano.
You'd Expect: Well, anything other than how they demonstrate it below.
Which Is: Rigging the volcano to have real lava squirt out of it.
Even Worse: King Koopa intervenes and accidentally causes Hop to release huge amounts of lava.
The Result: The school becomes destroyed and Princess Peach ultimately expels Hip and Hop.
While All This Has Been Going On: The Piranha Plant that Hip and Hop planted to sabotage Oogtar's "eggabaga" project grows large when Oogtar adds fertilizer to get an edge over Hip and Hop's volcano. During the chaos that ensued when the volcano errupted, the Piranha Plant runs out of the school and eats Koopa, Hip, and Hop. Yoshi then walks up and eats the Piranha Plant. He sits there with a bloated stomach, complaining that he doesn't feel good.
You'd Expect: Mario et al to encourage Yoshi to deal with it and let him digest, thus effectively killing off their archenemy and 2/7ths of his children.
Instead: The Princess directs Yoshi to inexplicably spit Koopa, Hip and Hop (who logically should still be inside the Piranha Plant) into a pipe.