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.
At the beginning of episode 67, when eating the rice balls Kotori had given him while in Zexal mode, Yuma is basically able to share them with Astral. Since Astral doesn't normally eat, this is a new experience for him and he really enjoys it, commenting that it must be how it feels to truly be alive and that it's really fun being with Yuma.
Episode 80. When Alito confesses to Girag 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. Alito is injured and Girag 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 Girag's rage over the attack on Alito and his determination to take revenge, utterly trusting in Alito'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. Girag is fighting so hard for Alito's sake. Also doubles as a tearjerker.
Epsiode 98. Yuma managing to bring Astral back to his senses by hugging him, undoing the Dark Zexal form Astral had initiated while under the influence of the darkness, and then when Yuma and Astral reconcile, touching the palms of their hands together before initiating their new Zexal II form.
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.
In Episode 138, Vector is being dragged towards Don Thousand, who intends to absorb him. Yuma immediately runs forward and catches his hand, trying to save Vector despite everything. He insists that the true Vector is Rei Shingetsu, and despite Nasch and Astral both urging him to just abandon Vector, he refuses to. Vector declares that he's taking Yuma with him, only for Yuma to reply that that's fine and that Vector isn't alone. He cries a single tear and it hits Vector's face, shocking him. Stunned, Vector decides that he can't drag Yuma down with him, and lets go of Yuma's hand, letting himself be absorbed.
The fact that Yuma actually wins his duel against Nasch accidentally because he refused to attack his friend!