A more minor example, but Freedom Planet 2 reveals that even since gaining friends in Lilac and Carol, Milla still keeps Mr. Stumpy, her old Companion Cube from her Friendless Background days, around; taking him up and replanting him just outside the front of her house.
After Milla defeats the Kakugan mech in Avian Museum, she almost immediately sees Aaa as cute, and becomes apologetic for wrecking his mech. Even though she was meant to arrest him, she doesn't take any cruel stuff to him well, such as when she saw it mean to abandon Aaa without Syntax. It becomes sweeter when she finally befriends him and the pair become science buddies, due to their shared love of science.
Corazon, despite the task she's to undertake for Merga, still cares about her younger sister, Carol, a lot, which is proven by her ordering Aaa to stand down and that she's not at the same threat level as the other heroines in her eyes. In fact, the whole reason she was even working for Merga in the first place was because she was promised protection for her and her family when Bakunawa rose.
Before Gravity Bubble, Carol tries to apologize to the others for running off. Milla readily accepts it, but points out that Neera was actually the one whose feelings were hurt the most. Carol takes this to heart and apologizes and explains herself to Neera in earnest. Though Neera initially is bothered that Carol was told about how upset she was, she appears appreciative of Carol's words.
Carol: Scary l— Neera. I'm... sorry for leaving you behind. But not for chasing my sister. I had to do that, y'know? Cory's an annoying brat who keeps running off because of stuff she just won't EXPLAIN... but she's family. You understand, right?
In Lilac's story at Shuigang Palace, or Milla's story after the Robot Graveyard, Lilac asks Milla if she wants to sit the mission out, as if to imply she's willing to take it on for Milla's well-being; this becomes important when it becomes clear Brevon's robotic remnant is operating out of this area. Likewise, at Nalao Lake (unless you're playing Carol), she affirms to the pup that she can talk about her issues at any time, whether Serpentine brought it up or not. Lilac cares for her friend, and Milla needs that shoulder, because...
After spending much of the adventure anxious and nervous over the idea that her whole existence is actually just to be a weapon for Brevon, Serpentine spills the beans to Milla's friends at the end of Inversion Dynamo. Without even the slightest hesitation, everyone assures Milla that they don't doubt her in the slightest. Most notably Neera, who had been grappling with trust issues and wavering loyalty for much of the game, is the first to speak in Milla's defense.
Milla: I guess it's true about me not being from this planet... But I'm not a traitor! I'm... I'm not a monster... Neera: I already know. Lilac: No. You're not. You're my friend, and you're wonderful. Carol: That's right. Whatever the opposite of a monster is, that's what you are!
Especially heartwarming is that, if Neera Li is the protagonist, she'll just quietly smile following the boss fight with Serpentine after Milla thanks her once again for trusting her. Neera and Milla spend the most time together in their stories, forming something of a secondary pair like with Carol and Lilac, and the bond they've formed fighting Merga together has grown incredibly strong. It's at this point the two really, truly become friends, starting with Neera gently teasing Milla about filing those reports on her experiments and Milla actually acquiescing.
A very small moment compared to any of the above, but if you start restoration on the Beast mechs in the Museum, Maria Notte shows up to do a report on their particular restoration... and yet, in the midst of the initial pitch, she whispers to you that she's omitting you from the report to avoid being banned from the museum, and she clearly knows you're responsible. Sounds a little backhanded like that, but she really does appreciate your work.
