At the beginning of the movie, we see that Tony, in the midst of the Underminer attack, found out that Violet, the same girl he was planning on taking to the movies a little while prior, was a superhero. Before she could explain herself, a scared and confused Tony ends up running away from the incident. When confronted by Rick Dicker, he expresses shame that he just ran away without hearing her out and just wants the whole incident to be forgotten. He does...as well as everything else about Violet.
Violet cringes when she reveals she unmasked herself in front of her crush to her parents in the paddy wagon. She sounds like she is on the verge of tears with guilt, and her facial expression sells it.
When Helen so much as suggests Bob try getting back his old job, the latter tiredly says he'd rather not. It's very telling that he'd rather keep job-hunting than retread what he had to go through: a depressing job at a corrupt insurance company with a boring environment full of cookie-cutter co-workers, and a toxic boss to boot.
The Screenslaver's motivations for wanting supers to remain illegal. When there was a break in, Evelyn's father opted to call up a superhero, which caused him to get killed. Evelyn's mother died soon afterward out of grief. As such, Screenslaver seemingly has a more understandable reason for hating supers in comparison with Syndrome's more petty justification.
There are moments where Evelyn betrays a bitter yet grieving expression while talking about how her father died waiting for superheroes to come and save him. Despite everything that she's done and is about to do, she still has humanizing qualities that makes one feel at least sorry for her.
Crossing over into Fridge Horror, it makes Bob's Speech Harsher in Hindsight. He encouraged Helen to be Elastigirl again to promote Superheroes, so their kids could have the choice to be superheroes. And the person they depended on to deliver on that promise (Evelyn) was planning all along to make it so superheroes becoming legal again would not be an option. Evelyn's speech about how Elastigirl was too trusting in the former making her hopes possible also becomes a scathing Jerkass Has a Point moment.
Bob hearing that Elastigirl is being praised so much that he feels inadequate as a parent.
Bob watching on TV his wife's train rescue becomes Harsher in Hindsight when you remember the reaction people had the last time he did the same.
Tony having his mind wiped out leads to him missing out on his date with Violet, without the latter knowing what happened. Violet spends the evening heart-broken, and after she found the confidence to talk to him. After being relocated, it was probably the only happy thing she had to look forward to her in her drastically changing life...
To say nothing about how Violet hurts over her crush now not knowing her is like having someone you had a crush on break up with you, but you haven't had even a date with that special somebody. It's enough to make Violet attempt to rip up her suit (Keyword "attempt" note it's Nigh-Indestructible since it was designed by Edna) and renounce being a Super.
How she finds out what happened. Bob tells her the truth, and instead of making her feel better like he hoped, it only makes things worse, as she is now furious with him, and it leads to the above-mentioned 10-Minute Retirement.
Bob: It's best that he forgets. It's better for you, too. I mean, I can't tell you how many memories Dicker had to erase over the years... when someone figured out your mother's or my identity. Violet: It was DICKER! YOU TOLD HIM ABOUT TONY! Bob: Honey Violet: YOU HAD ME ERASED FROM TONYS MIND!!!
Then Bob tries to make it up to Violet by taking her to the restaurant where Tony works, but it still doesn't restore Violet and Tony's relationship due to an embarrassing "water through the nose" moment on Violet's part, as well as Bob and Dash coming on too strong. Violet only gets a happy ending with Tony by mustering up the courage to just directly talk to him again at the very end.
While not an apparently sad moment, there's the context of Bob realizing his Incredibile is being auctioned on TV, and after he was told it was destroyed when supers went into hiding. For him, it's like being told your sibling died, and then years later, realizing that not only are they alive, but they're being sold to somebody.
The program that relocates Superheroes being shut down. Rick Dicker's gloomy disposition couldn't be any more fitting, given that not only does it mean he loses his job, but superheroes won't have an affordable way to hide anymore.
In a meta-example: Rick Dicker saying his goodbyes to the Parrs and his It Has Been an Honor line, can be a bit hard for those that remember that Bud Luckey had voiced him in the first film and he passed away before the film came out (the film is also dedicated to him).
And later, there's a sense of helplessness as one watches the hypnotized Mr. Incredible, Frozone and Elastigirl give a televised speech of how bitter they are. Imagine how devastating it must've been for the people to see the much beloved supers return from shadows, only to seemingly go bad and burn bridges.
Winston's understandably shocked and conflicted expression upon realizing his sister's villainous scheme.
How did Gazerbeam and Fironic react to Mr. Deavor's death given he was one of their best friends who they'd given a phone to call them explicitly to protect him? Even worse given at least Gazerbeam was killed by Syndrome.
Notice how out of the supers that Winston managed to round up, Elastigirl didn't recognize any of them. You'd think that with her becoming active again some of the older heroes would take the opportunity to come out of hiding until you remember that most, if not all of the old supers that Mr. Incredible, Elastigirl and Frozone knew were killed by Syndrome's Omnidroids.
In a deleted scene, there is a memorial for all the supers that Syndrome killed. During the memorial, Bob gives a very heartbreaking eulogy about Gazerbeam and his origins. When he discovered his powers, he felt like a total freak and just wanted to be normal, until the Supers encouraged him to embrace his uniqueness by joining the Supers. When the Supers had to go underground, Gazerbeam decided to fight for the rights for Supers everywhere, but couldn't adapt to civilian life (as Bob noted when reading the paper in the first film). Then, when Syndrome started killing off all veteran Supers one-by-one, Gazerbeam went underground and used the last of his strength to write down a clue so others wouldn't fall victim to this, right before he died. Bob then tells the people how they must keep having hope on the Supers being allowed back into the world.
If the context of Bob and Lucius' conversation in the first film about Gazerbeam is really looked into, it would seem that Gazerbeam was one of their closest friends and they never saw him again when the Supers left.
In another deleted scene, the Parrs go over to Kari's house to ask her about Jack-Jack and why he was acting strange. Sadly, Kari can't tell them anything since Dicker erased her memory of Jack-Jack's powers and Syndrome arriving at the house. What's worse is that Kari's father doesn't care that the Parr's house was blown up and that they are homeless, due to them believing that they caused Kari to go mental. After slamming the door in Bob and Helen's faces, Kari's parents can be heard fighting over the Parr's predicament and what happened with Kari.