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...
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.
Aladdin is taken in by a suspicious creepy old man who shows up in his jail cell, despite being pretty savvy and street-smart up to and after this point, just because he has to in order to facilitate the plot/genie.
Given how harsh the law seems to be in Agrabah, I.E. getting your hand cut off for stealing, the penalty for kidnapping the princess is almost certainly death. Aladdin was going with the option that looked less likely to get him killed.
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.