- The montage of the boxtrolls growing less in numbers as the red hats capture more and more of their kind. The music playing then gradually falls into a Mood Whiplash. All the while, Eggs grows sad at seeing his friends face this crisis on a nightly basis.
- Eggs' depression when Fish is captured, and his frustration that the boxtrolls are too cowardly to try saving him.
- When Winnie points out that Eggs is a human, and Eggs protests he's a boxtroll, look at Fish's expression. It's a blink-and-you'll-miss moment. He looks guiltily to the side, indicating he never told Eggs the truth about how he's human. The other boxtrolls just nervously agree with Eggs, unready to admit they haven't been honest with the him.
- When Eggs looks to Fish to tell Winnie he is a boxtroll, Fish sadly shakes his head no.
- The truth about the Trubshaw Baby legend. Mr. Trubshaw was a friendly inventor who found kindred spirits in the boxtrolls. When Snatcher came to coerce Trubshaw into building a weapon by threatening his son, baby Eggs, the inventor immediately gave Eggs to the box trolls for safe-keeping before Snatcher knocked him out.
- When Winnie describes to Eggs what a father is like, she starts to name off all the qualities of a good father. (They play with you, love you, comfort you when you're scared of the dark, always listen to you, and are never too busy for you.) Her expression grows downcast, as though she's admitting to herself she grew up with a father who is none of those things.
- Egg's disillusioned attitude after failing to tell Winnie's father the boxtrolls are friendly. He bitterly claims how selfish and uncaring humans are. He and Winnie depart with heavy hearts.
- Before this, his being wrongfully scolded by Lord Portly-Rind (for sending his prized giant cheesewheel into the river) can be pretty depressing when you bear in mind Eggs looked to him as the only father figure he could turn to. From what he heard, fathers are capable of solving your problems, and he truly hoped Lord Portly-Rind would be such a father. But rather than listening Egg's announcement that he's the missing Trubshaw Baby, he shames Eggs, and over a wheel of cheese no less. So Eggs is forced to leave the party note .
- When Eggs warns the boxtrolls they must evacuate their home, the boxtrolls hide in their boxes. Fish politely offers Eggs the latter's box. But disgusted with their cowardice, Eggs angrily rebuffs "NO I'M NOT A BOXTROLL!" and backhands the box away. Hurt, Fish cowers into his box, looking at Eggs as though he were one of the humans. It's every parent's worst nightmare for their children to act violently. Thankfully, they get better towards the end.
- The destruction of the Boxtroll cave, Egg's childhood home.
- Before lashing out at the red hats, Fish is mortified to see Eggs knocked unconscious in his attempt to save Fish.
- Eggs crying after watching the Boxtrolls be crushed. Thankfully, they are revealed to be fine.
- A small one near the end when Mr. Snatcher finally gets a white hat and eats cheese in the tasting room. Before he can eat the piece of super-tasty cheese, Eggs tries to talk him out of it, saying it won't change who he is. Mr. Snatcher (who at this point is freakishly swollen due to his cheese allergy) looks at him with a look of desperation, lip quivering and single eye watering as if to say "all I want in life is to be important and respected; is that so much to ask?" True, he is a cruel and despicable man, but in his allergy-riddled state it's hard not to feel a little bit sorry for him. The way he looks at the cheese and sweats as he starts to taste it, it's as if he has a moment of clarity that he knows he may die doing this, but he can't stop now because it's literally all he's ever wanted.Eggs:: Cheese, hats, boxes...they don't make you. You make you.Snatcher: (momentary look of sadness before his expression hardens) I have made me, boy. This is my destiny...
- Even Snatcher's death is pretty sad when you think about. He only wanted to become a white hat so he could be somebody and gain respect. Yet in the end, Snatcher ends up killing himself, having been corrupted by his own ambitions.
Tear Jerker / The Boxtrolls