Ash wanting to go back for the sinking cage full of Pokémon from the St. Anne despite the fact that he's in danger of hypothermia. His subdued demeanor on the surface when Pidgeotto finds him and Squirtle speaks volumes about how he felt leaving them there. Luckily, Krabby's evolution into Kingler allowed him to save the cage by himself.
The reveal that Charmander is still afraid of being abandoned by Ash since he's (comparitively) weaker than a majority of the team. Even after leaving Damian, who he had so much faith in, now he has a new fear of abandonment.
Chapter 24 has Butterfree's mate being captured by Team Rocket before he even arrived, with the Rockets setting up a switch beforehand with Ditto. The follow-up chapter is completely dedicated to the aftermath, particularly Ash's grief.
During Chapter 27, Gengar is lashing out in anger at the loss of Gastly to Team Rocket, controlling the entire Pokémon Tower and twisting the surroundings to ward off humans, at the same time having Haunter attack the people of Lavender Town. When Ash has his soul pulled out by Haunter and is taken to him, it's revealed that he's controlling it from the playroom, specifically the swing that was Gastly's favorite in canon.
Psyduck's reason for locking up his powers: Some terrible accident that he refuses to speak of in detail left him without a home to return to. He's still afraid of his own power, even with Drowzee's tutelage.
Chapter 32 reveals that nearly a week after the fact, Butterfree was still haunted with nightmares revolving around what could be happening to his would-be mate, unable to tell if they were fabrications or some latent ability to receive visions.