Flik and Dot's friendship throughout the movie is nothing short of sweet itself. Dot is the first one to show any genuine appreciation for Flik's inventive ideas, and she's the only one who still believes in him when he gets exiled from the colony for his "warrior bugs" deception.
"Well, Flik, you really goofed up... thanks." Followed by the circus bugs and the entire colony applauding. Flik is understandably teary-eyed.
In all the colony, out of all the countless ants, it's not the elders or the Council or even the Queen who speaks up when Dot is being threatened. It's Flik, the outcast.
"Leave her alone!"
Flik and the circus bugs rescuing Dot from the goldfinch. Followed by:
Rosie: W-What is that?
Manny: That my friends, is the sound of applause!
Gypsy's tendency to gently rub Manny's hand when he's feeling down. The quiet love between them is tangible whenever they're onscreen together and it's not a CMOF.
The two young ants who want the circus bugs' autographs.
"When I grow up, I want to be a praying mantis!"
"I want to be a stick bug!"
"Oh, they're all so cool—I can't pick!"
While it doubles as a CMOF, Rosie's horror when she realizes she actually hurt Dim and the fact that she immediately rushes to comfort him regardless of P.T's anger.
The scene in the circus van, with Flik's friends reminding him of the good he's done.
And before that (though it crosses with a Tearjerker), her desperate "Dot! Dot! Has anyone seen Dot?" Especially heartwarming given their rocky relationship up to that point.
And the first thing Atta says to Flik when he inspires the other ants to stand up to Hopper with his "Ants don't serve grasshoppers" speech? "I'm so proud of you, Flik!" After all the times she's been anything but patient with Flik, especially the part where she banishes him and the circus bugs, that one moment there officially cements her newfound respect for him. It soon becomes even sweeter when she shows genuine concern for him when he goes to lure Hopper to the bird's nest to be eaten.
"Sorry. My place is here."
Francis catching Dot mid-fall. Bear in mind, he's been established as the Token Jerkass Teammate, yet when he sees a small child screaming for help, his first instinct is to save her.
Also, his bonding with the Blueberry Scouts, and the kids all hugging him tight as they all say goodbye.