In the first game, Dr. Cain uses Dr. Light's designs for X to create Reploids. These robots are missing design elements that Dr. Cain couldn't understand and haven't gone through the testing period X did to ensure his safety. You'd expect: Dr. Cain to make sure that the Reploids were as safe as possible by not doing things like giving them special powers or built-in weapons, making them stupidly huge, and keeping them human shaped. Maybe a hidden set of computer commands that can track and paralyze them from a safe distance. They are robots after all. Instead: He goes nuts building the Reploids, who eventually go nuts on humanity. In Addition: Nobody thinks to start installing actual security measures into Reploids until X8. They attempt this by using copy chips - chips that contain DNA data of hundreds of existing Reploids - that can change a Reploid's DNA and grant them immunity to the Sigma Virus. But nobody bothered to check what kinds of data were encoded in them, so it wasn't until the events of the game that they found the chips had copies of Sigma's DNA data—which is the virus causing Reploids to go Maverick—installed. Which not only allows them to go Maverick at will, but to steal the identity of anyone they damn well please.
Going further is the world's reaction to this incident. After the incident, the government shuts down all copy chip research because it's pretty obvious those chips are hell in micro form. You'd expect: That everyone would heed that lesson, never manufacture copy chips again (or at least double check which Reploid data is programmed into them), cancel anything and everything that actually needs these copy-generation Reploids to function properly, oh, and kill all the copy-gen 'roids, or at least keep them under very close scrutiny if they do have a problem with mass executions. Instead: Not only are we NOT told that all of the copy chip Reploids are destroyed, but people are so obsessed with building their ungodly space towers that they eventually put research into these chips BACK UP in spite of the warnings from people who pay attention to history. If Command Mission is anything to go by, they basically ASKED for Colonel Redips.
In Maverick Hunter X, X and Zero are investigating a string of mysterious incidents that are flaring across the city, including someone breaking a dangerous Maverick out of jail. Since Zero observes that the guards were defeated by a Reploid with very high combat abilities, he suspects that their commander Sigma must be behind it because he's one of the few Reploids with specs that high and he suspiciously cannot be contacted. You'd Expect: For Zero to tell X about his suspicions, just in case he's right and Sigma tries to back-stab them while they're trying to find the truth. Especially when he says he, 'has a bad feeling about this'. Instead: Zero says nothing to his friend, meaning that while he was ready for Sigma to betray them, X wasn't, and he was used as a hostage against X while his partner froze in hesitation and confusion. A few minutes later, both he and X are badly wounded, and Abel City has been blasted with missiles.
From the above two games: Vile has captured X using his Ride Armor, and a previously incapacitated Zero leaps onto the back the Armor, where Vile can't aim any attacks at all. There's no indication that Vile can't be shot directly, the original game uses Game Play And Story Segregation to prevent any easy headshots while the remake has Vile just grab X, preventing the fight altogether. You'd expect: Zero to aim his Z-Buster at the back of Vile's head and shoot it off. Zero's shown in the intro stage that he can tap his buster's full attack power much faster than X. That way it's two on one when it's time to fight Sigma. Instead: He self-destructs, destroying the armor and saving X, but killing himself in the process. Again, there's no reason to assume Vile is invulnerable when he's there. It's really blatant if this happens when you don't already have the buster upgrade, because Zero will give his own as he dies, showing that it's been fully functional the whole damn time.
In X2 X has to fight the X-Hunters to reclaim Zero's parts, except the control chip which the Maverick Hunters already have. Having Zero on either side is showed being very important. Canon dictates that there was a black-painted copy of Zero in the villains' possession. You'd expect: The X-Hunters to turn over the parts of the fake, and either rig them to explode in enemy HQ, or to take Zero's control chip back to them. Instead: They actually turn over Zero's parts, with no attempts to retake them at all.
The Repliforce army is held under suspicion for being responsible for the fall of Sky Lagoon, destroying an entire city and killing millions. The hero you're playing as comes across Colonel, a high-ranking member of Repliforce, in the ruins and asks him to disarm and come in for questioning. You'd expect Colonel to immediately disarm and come in for questioning, both in a show of good faith for the victims and to clear Repliforce's name. Or, if he believed that he/Repliforce would be unfairly treated for whatever reason (feels there's too much anti-Reploid prejudice, suspects there might be a frame job with too many people in the right places, believes that in the panic they might just get blamed anyway, etc), clearly mention that as a reason for refusing. Instead He declares that laying down his sword would be dishonorable and leaves the scene, causing all of Repliforce to be declared Mavericks and start a massive war. Even Worse To draw the Maverick Hunters away from Repliforce, Jet Stingray attacks and destroys a city, meaning they've now committed an act on the scale they were improperly declared Mavericks for in the first place.
X4 reveals Sigma and Zero fought when Sigma was a Maverick Hunter. At the time, Zero was an unidentified Maverick berserker who killed a whole hunter unit, and Sigma stepped in personally to take him out. They begin fighting, Sigma has his beam saber and Zero, for whatever reason, isn't using his Z-Buster and dash boots and runs like idiot intending to beat Sigma to death. You'd expect: Sigma, whose sole purpose at this point is to take out Mavericks as quickly as possible, immediately use his saber and chop his target into two or more pieces, winning in a Single-Stroke Battle. Instead: He plays around, ultimately getting a near fatal beating and becomes infected with the Maverick Virus, which leads to his becoming evil.
Also in X5, Lifesaver discovers ominous data that implies that Zero is heavily linked to The Virus somehow, since it increases his power output instead of hurting him. He reports this to Commander Signas, who wisely decides to keep this top secret for now and not to act rashly. You'd expect: Lifesaver to follow orders and go back to his job, trusting his level-headed commander to make the best decision on how to move forward, since he's just a medic. Instead: Lifesaver goes behind Signas' back and tells his suspicions to X, Zero's best friend, accusing Zero of being dangerous and points out that Zero is unaffected in an area brimming with The Virus. The resulting concern and mistrust between the two friends causes them to fight and nearly get killed by the Big Bad when he takes them by surprise. Lifesaver unsurprisingly hasn't been seen in the games ever since.