Alas, Poor Villain: A few when you realise they're fighting a needless war. For example, SaberLeomon and Merukimon. Merukimon's death in particular is tough to watch.
ProfessorAkihiroKurata is far and above the most despicable human villain to ever appear in the Digimon franchise, with his only goal being to Take Over the World and sadistically destroy all Digimon that he can't personally control all because of a grudge against Spencer Daimon and the Digimon he cared so much for. Creating the Gizumon, mechanical monstrosities that make other Digimon Deader Than Dead by stopping them from reincarnating like usual, having the heroes' memories wiped, blowing up DATS HQ and making the Data Squad into fugitives, and experimenting in creating half-Digimon hybrids were only the start for Kurata, as he then went on to craft a Weapon of Mass Destruction to kill thousands of Digimon on the continent of Eldradimon in one shot, forced the Teen Genius on the heroes' side to a Face Heel Turn by threatening to kill his Ill Girl little sister in an experiment, tried to replicate his hybrid experiments on said Ill Girl, and finally awakened a mighty Demon Lord in order to merge himself with it to destroy all of his enemies so that he could then wipe out all Digimon and have total control of both the Digital World and the human world. And his motives? PettyGreed, cowardice, prejudice, and Inferiority Superiority Complex.
Epileptic Trees: The dub director, Jeff Nimoy, believes that Yggdrasil/King Drasil was a computer created by Digimon Adventure's Izzy and the entire world was his simulation.
Funny Aneurysm Moment: The Digimon you would usually root for in the previous series[1], are bad guys, as members of the Royal Knights. Well, at least until the final battle.
ManyMonster of the Week Digimon were good guys in previous series. A lot of people were rather unhappy with seeing so many of their old favorites shoot at the good guys for a few minutes and then die. Examples include Digmon, Garurumon, Togemon, Garudamon and Zudomon. This goes into Fan Dumb territory when one realizes that Digimon were always portrayed as both individuals and members of a species, and that Digimon Adventure once used a second Greymon - the evolved form of the main character's digimon - as a Monster of the Week.
Good Is Dumb: Too often, the heroes just stand and watch Kurata's weaponry line up, and waste time openly wondering what he's up to instead of trying to prevent it. Given that his stated motive is Digimon extermination, it's hard to understand why they let his minions work away with little opposition. This is particularly prevalent during the Eldradimon siege.
Ho Yay: At least in the original, Lalamon gets a little too touchy when Ivan says he will become Yoshino's boyfriend. Then again, it's hand waved as Lalamon playing along Ivan as an excuse to distract him from commanding the Gizumon, but she does get some suggestive lines like "Don't worry, I won't hand you over that easily".
Then there's Touma's battle with Nanami. Touma seems to really ignore the half-naked Nanamis in favour of the powers even he cannot calculate (read: Masaru). As much as he doesn't get over being ignored because Masaru is today's designated saviour, that particular scene fired up the bipolar sensors.
Idiot Plot: Hashiba gives Kurata his support despite working with Satsuma and Yushima, who can both confirm that the man has open issues with authority, questionable mental stability and was responsible for compromising the original rescue mission in the Digital World. The whole Japanese Government takes this beyond reason by hand control of the entire military to a Kurata, even after he had committed an open act of terrorism by personally bombing DATS headquarters.
Jerkass Woobie: Nanami and Ivan of the Bio-Hybrids; Nanami when solemnly monologuing about how she's been lonely all her life due to being socially isolated because of her intellect, and Ivan when it's revealed that he only works for Kurata because he needs the money to support his many little brothers and sisters, and is too dim-witted to truly realize what he's doing is wrong.
Love to Hate: Fans sometimes praise the series for having a villain who is genuinely despicable and hateful, not least of all because watching him get his just desserts is so satisfying.
Magnificent Bastard: Nanami is a member of the Bio-Hybrid, a trio under the subservience of Akihiro Kurata. A genius who grew up isolated from everyone because of her prodigious intelligence, Nanami joined Kurata and hunted Digimon solely as an outlet to escape the droll in her life. Taking an interest in Thomas H. Norstein, Nanami undercuts his plan to protect the waterfall of the Sacred City located on ElDradimon by easily guessing where he'd be. Spending the entire scuffle against him and Gaomon predicting their every move with utter ease and mysterious grace, Nanami uses their shared experiences and her own dark charms to try and shake Thomas's faith in his friends. While undone by Thomas using a strategy unfathomable to both her and MirageGaogamon, Nanami still has the last laugh, gracefully accepting defeat only because she pushed Thomas into using someone else's power and tactics rather than his own, and uprooting Thomas's strategy by destroying the coveted waterfall.
Mind Rape: What Metal Phantomon does to Marcus,Thomas,and Yoshi,not too different from what happened to Jeri
Mis Blamed: No, Ikuto's Tarzan-speak was not added to the english dub; he spoke broken Japanese in the original version too.
Motive Decay: At first Kurata's goal is the elimination of all Digimon. Then he suddenly decides, screw that: he wants the cliched "world domination" too! This is debatable, however, as Kurata's motivation also derives from his jealousy and inferiority complex towards Masaru's father, so total control probably would be something he'd want to achieve through digimons' power.
Nausea Fuel: A great many things count, but most especially Kurata's head coming out of Belphemon's body.
The Scrappy: Justified example: Ahikiro Kurata, since his evil acts are outnumbered only by his Unwitting Instigator of Doom tendencies, and usually go hand in hand. His very motive for killing the Digimon was based on at least one act of cowardice on his part, which he's even told by Marcus but he's too much of a self-centered Jerkass to accept this.
Stupid Sacrifice: Baronmon stands on a wall, yelling out to the ships not to hurt Eldradimon, and gets shot in the back by a Gizumon XT. Even assuming the ships could hear him over that range, what made him think they'd comply, and why did he feel the need to expose himself to attack?
See Funny Aneurysm Moment, but many returning Digimon who fared less well in Savers than in previous series got this reaction. Piyomon/Biyomon arguably has it the worst, not least of all because the director made him male, subjected him to The Worf Effect, and made him much larger. Had he been another species, the fans would probably have viewed him as The Woobie, not hated him.
Unfortunate Character Design: The Savers redesign of Yatagaramon suffers from this. He has a white mane that really stands out thanks to his mostly black and purple design. Said mane is braided into a single rope that dangles freely with a bell to each side of it. Guess we should call the Savers version the four legged crow.
Values Dissonance: Within the franchise itself. Previous Digimon series had firmly established that humans should not put themselves in the path of an angry Digimon, especially if it's large enough to cause serious harm to you. In Savers however, Masaru can only put himself in danger. Agumon can't evolve without him risking life and limb.
The Woobie: There are at least three: Keenan, due to his tragic backstory and conflicting feelings over his own human-Digimon identity; Thomas, due to his family struggles and the loss of his mother; and Yoshino, who suffered from a severe childhood-rooted inferiority complex for the first third of the series.
Woolseyism: Masaru/Marcus makes a pun on Thomas/Touma's name when they first meet and calls him "Tonma". (This means something along the line of "Stupid" or "Fool") Because it's a Japanese pun, it doesn't translate well...however another nice pun works, too. In the English Dub, Marcus/Masaru calls him "Nerdstein", a pun on his last name. Doesn't have exactly the same meaning as the Japanese pun..but instead keeps the bit about Masaru making fun of Touma.