There is a spectacular one in The Dilgar War. In their one combat encounter with Earthforce, the heavy cruiser Persephone and her six fighters (of an outdated model that is about to be phased out for the new model) took down fifteen Dilgar ships between light cruisers and destroyers plus fighter support before charging at Jha'dur's flagship when the rest of the Dilgar fleet showed up and their jump engine was damaged. The Dilgar knew Earth Alliance already had a huge standing fleet that included ships that made the heavy cruiser look weak, and was building up. To reach the Vree Empire (that has already tried to stop their advance in the League), they have to choose between attacking the Markab, allies of Earth (and Earth Alliance made clear that attacking them would be an act of war), or the Yolu, more powerful than the Markab but isolationist and tactically incompetent: the Dilgar Warmaster Council voted to attack the Markab with a 5-4 majority (Jha'dur and the other competent Warmasters voted to attack the Yolu). Less than a month later, Earthforce has annihilated Jha'dur's veteran fleet (Jha'dur herself barely escaped with her life twice, first when her ship was in the firing arcs of fifty Earth dreadnoughts and then when Earthforce decided to finish the routed Dilgar fleet with five times the number of surviving Dilgar ships in nukes), and one of the other competent Warmasters is dead.
The Dilgar have a policy of attacking warships from neutral governments to make reparations and have an excuse to stipulate an alliance. While the policy had worked with the Narn, it failed miserably with the Earth Alliance. Yet, they kept it in place and hoped to get the chance to try it with the Minbari. The same Minbari that in a dozen years would utterly defeat Earthforce with little losses. Jha'dur had the sense to question the wisdom to try it with someone they knew was isolationist and incredibly powerful, but was ignored again.
In Arads Stardust, Dr. Vahlen's cold, provocative attitude when testing the cooperative Twilight Sparkle's abilities is really not the smartest one to take when she herself notes that X-Com couldn't hope to build anything that would stand up to Twilight's telekinetic blasts. Several characters note how stupid this is for the supposedly-bright scientist, and once Vahlen finally looks past her Freudian Excuse for her hostility, she also realizes how foolish her behavior was.
The Mega CrossoverHasbroverse uses this in its World Building backstory to explain why G.I. Joe disbanded: Cobra Commander, being based on his more competent Marvel Comics counterpart, was smart enough to avoid getting into a fight with the Decepticons. Serpentor, however, wasn't as bright, and launched an attack that pissed off Megatron enough to launch a counterattack so ferocious (including glassing Cobra Island) that only a handful of members of the organization survived — Cobra Commander himself, who was smart enough to flee when he realized what Serpentor had done (and now lives like a king somewhere in upstate New York); a half-dozen Mooks loyal enough that the Commander took them with him; Destro and The Baroness, who left the group some point prior; and Storm Shadow, who'd had a Heel-Face Turn and likewise left the group. There's also rumors that Zartan survived as well, but there's no confirmation of that.
Prof. Penthesilea:"…Carrie as you'll soon find out, warns us of the danger of underestimation, of messing with the wrong person and not treating everyone with the respect they fully deserve. While this may be tempting for some, it will be an insult to the one you abuse, and may end in your untimely death."
Kitten, after having been stopped nearly effortlessly by Jade in the Tournament of Villainesses (Jade used heat vision to blast away Kitten's energy whip and then picked her up with the Rooster Talisman), proceeds to insulther! The evil teen insulted Jade's outfit and appearance (the appearance part in multiple ways), her power set, and was starting to say that Jade was so ugly that that was why she wasn't in her original dimension, they had kicked her out (she didn't finish, but it's clear what she was saying), before Jade's Berserk Buttons were fully pressed and she unleashed a Dragon Talisman blast that nearly killed Kitten, giving Jade a My God, What Have I Done? moment (as, unlike the others Jade had met, the evil blonde was notMade of Iron). And this was AFTER Jade had offered Kitten a chance to surrender!
This happens literally in 3 Slytherin Marauders when a Death Eater attacks a dragon that has befriended Harry Potter — he got his Just Desserts, though the dragon later complained that he gave her indigestion.
In Seventh Horcrux, Harry Potter is accidentally possessed by a portion of Voldemort's soul when the killing curse rebounds. Then he is placed in the care of the Dursleys, who promptly treat him like in canon. That does not last long, as Voldemort/Harry promptly remembers how to use wandless magic and begins terrorizing them.
A lot of civilians in the Uplifted series seem to think that bullying the somewhat mentally unstable Waffen-SS Colonel Joachim Hoch is a perfectly rational thing to do. Very few survive his wrath unscathed.
Crisis Equestria, has this. In Chapter 17, Tick Tock says things that extremely piss off Starlight Shadow, which was part of Tick Tock's plan. It fails.
In Progress, Angel Bunny attacks Princess Luna with baseballs, knowing full well who she is. She freaks out at first, but after a little therapy with Fluttershy and Applebloom, she tries to keep cool about it until he breaks her glasses. Then she snaps.
In Running From Myself two former classmates of Twilight Sparkle mock her and call her names in front of everypony like they used to, even while knowing she is Princess Celestia's personal student, and thus capable of great magical powers.
This was true in a non-violent way when they were fillies. They never seemed to think that bullying somepony that Celestia holds dear would result in their suspension. Suspensions that they, naturally, blame on Twilight.
In The Vinyl Scratch Tapes Vinyl callsPrincess Celestiaout during a live broadcast interview for the whole "banishing your sister to the moon and never checking up on her even once for a thousand years" thing. Her co-host Octavia is horrified by Vinyl's behavior and is stunned when Celestia accepts it with good grace instead of having them immediately yanked off the air and thrown into prison.
This comes back to bite Vinyl big time, when Princess Luna royally chews her out for giving Celestia a huge guilt trip over the incident when it was entirely Luna's fault to begin with and she had no other choice but to banish her.
Barako: I would like to file a complaint against Uzumaki Naruto.
Ninja Clerk (grabs a pen and a form): What is the nature of this complaint?
Barako: That filthy little monster threatened to break my daughter's arm!
Clerk (fills in information): Where were you, and what were you doing at the time this threat was made, and at what time did it occur?
Sakura: I was outside the Academy. I had just gotten out of class for the day, and noticed him hanging around on that swing in the tree near the entrance. I...I tried to hit him.
Clerk (coldly crumples form): Let me get this straight. You, an Academy student, decided to attack a full-fledged shinobi who is only a Genin because he had a run of seriously bad luck, and isn't currently on his way to the Chunin exams because we don't want to give Iwa a chance to legally get their revenge on him for what he did to two of their Genin, and you want us to punish him because he decided to go easy on you and let you off with a warning?
In Kitsune no Ken: Fist of the Fox, Naruto gets subjected to this from the very first chapter, upon his arrival in Konoha Town in fact, by Mizuki's biker gang. Dosu, Zaku, and Kin, who'd previously had a run-in with Naruto at Ino's family greengrocery and had then dismissed him as being no threat to them, happen upon him later that same day and decide it's going to be a good idea to have the gang beat on him for kicks. The thing is, Naruto's a former member of the Kyuushingai, nine verydangerouspeople who laid waste to entire cities single-handedly over a 365-day period. The end result of the gang's attempt to bully him? Their motorcycles get turned into scrap, and several of their members wind up bloodied and broken on the ground. Then in the next two chapters, they have another confrontation, at which point he reveals his past to everyone present, and Mizuki (who's there this time) decides to send his gang at Naruto anyway. End result? Naruto defeats the whole lot of them with a soda bottle.
No Sues in this case, just the MSN Gang picking on Brandon repeatedly in Pokeumans. At first he was just getting in their way, but after a while It's Personal. This turns out to have been a really bad idea for them later on.
Of Love and Bunnies has a ship full of troobian soldiers chasing the Lost Galaxy Rangers... while they're on their way to a Kegger. For every Power Ranger on Earth. It ends exactly as well as you are thinking.
In Skies of Vermillion (a Transformers fanfic inspired by Ancient Rome), Soundwave purchases Tracks as a slave. Throughout the story, Tracks snaps at him, makes accusations, and even hits him on one occasion. Granted, Tracks has a Dark and Troubled Past, but the fact remains, Soundwave is his owner, and could easily have him a) beaten, b) executed, c) executed by being beaten, or d) beaten and then executed if he wanted to.