Shark "returning the favor" to Yuma by refusing to hand over the Ou's Key to Kaito and dueling him to keep it away from him.
Kaito, although an antagonist, shows he really does care about his younger brother when they interact.
Yuma and Astral's friendship and concern for each other is really sweet.
In episode 50 Droite finds out Kaito's photon change is killing him and she asks him to drop out of the tournament for his own safety. The genuine concern she shows for him is quite touching when you remember Droite's usual disposition.
Droite smiling when Gauche manages to defeat Fuya in episode 45.
Episode 80. When Alit confesses to Gilag his love for Kotori, rather than making fun of him, he actually supported and tells him to impress her. Considering how many past Yu-Gi-Oh! villains were perfectly willing to betray and/or harm others around them, that is saying something.
Episode 85 has something that's rather heartwarming in hindsight; Yuma and Rei, on their way to school, run into a group of Barian-brainwashed students, who are obviously after Yuma. Yuma could have stayed to fight them - especially since a group that large would have attracted his other friends to help soon enough - but instead, he chooses to protect Rei and they both flee.
Episode 87. Alit is injured and Gilag is more than willing to avenge his friend.
Part of what's great about 87 is that we have the heartwarming moments on both sides; the protagonists and antagonists. We have Gilag's rage over the attack on Alit and his determination to take revenge, utterly trusting in Alit's judgment on who did it. In addition, we have Yuma's absolute faith that Rei wasn't responsible, and his refusal to stop protecting him in the duel, even though Rei's play style is practically suicidal and Astral urges him to stop.
Episode 88. Gilag is fighting so hard for Alit's sake. Also doubles as a tearjerker.
Epsiode 98. Just Astral and Yuma.
Episode 121. When Astral is saved after Yuma defeats Eliphas.
The sixth ending theme, CHALLENGE THE GAME, it shows all of Yuma's allies supporting him, and even better, shows some of the show's villains looking content and happy in a benign way, and the song ends with everyone cheering on a friendly duel between Yuma and Astal.