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 massive, and keeping them humanoid. Ideally, they'd be issued weapons as needed from the government, and be given select tools and powers for the job at hand as opposed to constant access to such power. Since they're obviously supposed to be people, they should look like people so humans would be easily able to accept them as people, and they wouldn't feel so separate from humans with their radically different physiologies, as opposed to huge animal forms that would only serve to make a bigger gap between both species, instilling fear, jealousy, mistrust, etc. In case of emergencies, he could also make special electrical weaponry designed to shut them down their brains temporarily, essentially a high-tech tranquilizer for mechanical organisms. Instead: He goes nuts building the Reploids, who eventually go nuts on humanity, thanks to the Maverick Virus. 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,note not just in the sense of making Maverick decisions resulting from circuit breaks, abstract reasoning, misinterpretation of duty, etc., as all Reploids technically can do as they have free will, but in a sense akin to turning off their conscience at will, effectively becoming Reploid sociopaths, 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.
While Colonel definitely takes the cake in idiocy, Zero's handling of the situation isn't exactly graceful. He's just saved Colonel's sister, and received his thanks, but the situation does look pretty bad, and his superiors have already been suspicious of the Repliforce for some time. You'd expect: He'd ply him with assurances, like admitting that it's unlikely Colonel was involved in the attack, but as a member of the primary anti-Maverick force in the world it's his duty to make sure. Instead: He asks pretty bluntly if they were involved, to which Colonel says they came only to help. Now: It'd be the time to break the news to him as gently as possible, and appeal to his sense of honor and justice. He could simply tell him as a fellow soldier he must know that it's the sensible decision to have a full investigation. If Colonel shows hesitancy, he could ask him to do it as a personal favor for saving his sister. Instead: He drops a bomb on him.
Zero: They suspect you've become a Maverick. Colonel: What!? Zero:Disarm and come with me to HQ. The result: Colonel flies off the handle, insisting war would be preferable to the shame of accusations and surrender, and teleports back to General and prepares for war.
Colonel's What An Idiot moment is, for the most part because of a What An Idiot moment itself. Before X4, the government wanted to replicate the success of the Maverick Hunters and create a warrior as powerful as he was compassionate, just like X. Unfortunately, they were unable to achieve their goal, and were forced to spit the program they'd made into what became Colonel and Iris, the former a proud and honorable warrior, the latter his compassionate and sensitive sister. You'd Expect: They'd remember X himself went through 30 years of testing and that being careless with the design and conditioning of the artificial brains of reploids resulted in the original Mavericks, and notably the psychotic and murderous Vile, so they would put them through extensive therapy and analysis, making certain to teach Colonel that there is a time when pride must be discarded, and to teach Iris how to deal with emotional trauma, helping them overcome their greatest potential weaknesses. Instead: They decide not to bother, and immediately assign them to positions where they're directly involved in the Maverick Wars, Iris as a Navigator for the Maverick Hunters, and Colonel as the Colonel of the Repliforce. When Colonel is informed that his superiors, the government, think he's a Maverick, he's shocked at first, yet after hearing he'll be brought to HQ and simply questioned,(notably after disarming) suddenly becomes furious and rebels, and whenever seen, he comes off as almost delusional in his statements, insisting war is the only choice. He adamantly refuses to listen to reason, and in the end, is killed in a duel with Zero. Iris, after hearing the news, has a complete mental breakdown, uses her brother's chip to turn into a mech-like form to kill Zero, her body rejecting it throughout the battle, and she dies in Zero's arms.
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.