Regardless of her ultimate intentions, it's clear from their interactions that Arecia does care about Class Zero. Every interaction between her and any of the twelve Classmates shows the bond between parent and child, and with the exception of Tempus Finis, she is always wearing a smile when speaking with her children. Pay attention to it, and it's beautiful.
During the endgame, after everyone gets 'Condemned' by Cid during the last Crucible, they're all covered in blood to various degrees. Ace is distinct in that there's a trail from beneath his hairline, past his left eye and down his face - similar to the feather tattoo Izana has.
The flag in the ending, it's made entirely out of Class Zero's capes that are tied to their weapons.
The alternate ending in general. Everyone is leading happier lives in a world where the Crystals are erased from history. Machina even becomes best friends with Ace, since Izana is alive and dating Emina (much to Nine's chagrin).
In Chapter 7, when King and Seven ask Mutsuki for help on an offscreen mission. They are impressed by her skills in bombs and tell her they will come to her for help if they need to again.
Also in Chapter 7, when Ryid tells Trey and Sice he's considered unfit for battle, they tell him he can help people by teaching them survival skills, rather than just by fighting. He decides to take their advice.
As much a Tear Jerker as it is Class Zero comforting each other before they die.
In a scene that only unlocks in the Rubicus, Rem convincing Clemente to not give up and die just because she is the last member of the Five-Star guard.