The baby crocs in "Mom of a Croc". And the way they're calling for their mother.
Any time Blur appears. The first time, she's chasing Chris (who's an antelope thanks to his Creature Suit) and decides to cuddle him. Then there's also the time where she's with her son.
In "Flight of the Pollinators" a miniturized Chris goes missing after getting stuck to a bee due to being covered in pollen. Throughout the episode, Martin expresses guilt over letting it happen and worry for his brother's safety as he searches for him.
The Wild Kratts sending Donita the faux spider silk to use in her dresses, even after everything she's done to them.
From "Race for the Hippo Disk", Chris being genuinely concerned about Zach after he almost fell into a hippo's mouth (although we wouldn't expect anything less from the Bros).
Chris: Whoa. You okay?
In "Bat in the Brownies", Koki start feeling sorry for the bats when their tree home is destroyed. She immediately helps in the efforts of giving them new homes. And even lets builds a bathouse for Bitesize.
In an episode concerning Elf Owls: After spending an entire night using the owl's creature powers to find a missing Koki and Jimmy Z, the Kratt Bros cuddle up with an Elf Owl in a cactus. It's heartwarmingly adorable.
Admit it, tropers — Bandito, the black-footed ferret from...well, Bandito: The Black-Footed Ferret, had you going "DAWWWWWWW..." the moment you saw him.
Huge-O the orangutan shows up right when the brothers need Orangutan Powers, and the Kratts start disagreeing about whether the ape came on purpose or just by luck ... and then Huge-O holds out both hands, palm forward, to let them touch him. He definitely knows what's going on, and trusts the bros to save his forest.
In "Roadrunner", when a gila monster bites Martin's boot, Koki and Jimmy Z drop everything they're doing and rush out to assist what they believe to be a serious medical emergency. It's Played for Laughs because the lizard didn't actually penetrate the boot, and they wrap Martin in bandages like a mummy so he can't explain this, but it's touching to see just how frightened for their teammate his "rescuers" are.