Martin to an extent, for having run away from home out of jealousy of Timmy even when NIMH was still about searching for the rats.
Everybody in Thorn Valley, for having been so eager to fashion Timmy into a hero because of Nicodemus' warning of worse things yet to come from NIMH; ironically, their actions in reverence to this prophecy may have inadvertently put their home at even greater risk than it otherwise would've been; see Self-Fulfilling Prophecy on the film's page.
Thumbelina. Every time she gets kidnapped, she keeps letting the kidnappers take advantage of her. She could be excused since she's lived a sheltered life, but common sense should have stepped in at some point and while she does eventually stand up for herself, it's not until the last ten minutes of the movie. Yeah...
Let's not even get in to her not asking that goddamn bird to fly her home but instead trying to walk it.
Mickey, Donald, Goofy: The Three Musketeers has Mickey getting this temporarily when confronting Pete about his wrongdoing. He stands tall and alone against someone much bigger and stronger than he is instead of making a strategic retreat to get Goofy (who he doesn't know has been captured) or some other reinforcements.
In Rugrats Go Wild!, Spike seems to be pretty clever for a dog. He spends a musical number dodging and humiliating a huge leopard... but then he stupidly mentions that there's a group of lost, helpless infants somewhere on the island, and the leopard immediately goes looking for them to eat them.
In Rise of the Guardians, Jack falls for Pitch's Batman Gambit, and searches through Pitch's lair, looking for his teeth. When he finds the teeth, and returns to the other Guardians, the others immediately come to the (admittedly reasonable) conclusion that Jack is in league with Pitch. Clearly, Jack found the teeth and the idiot ball in the lair, because at no point does Jack attempt to explain, and the whole thing could have been avoided with one sentence. "I found where pitch is keeping the tooth fairies."
In Race for Your Life, Charlie Brown, it's Peppermint Patty's diplomatic voting. For one thing, it's massively one-sided: it only deals with the girls and their decisions end up screwing over the boys (including kicking out the boys out of the house that they found and leaving them in the snow). Second of all, the things they vote for is things that would require simple common sense. Of course, it's Peppermint Patty — common sense and that girl never got along.