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Modern Warfare 2 has a horrible research failure. Long story short: The shockwave from a nuclear bomb detonated in space destroys the International Space Station. Let's skip the part of an "explosion" in space and skip to the shockwave, this can't work for reasons anyone over the age of 4 can likely tell you there is no air in space (it's been argued that its the EMP that hits the ISS, which is even stupider because it blows the ISS to pieces instead of you know, being an EMP?).
The ending of Call of Duty: Ghosts. After pursuing Gabriel Rorke through a train and intentionally launching an ODIN strike on their position to drive the train into a lake, Hesh and Logan successfully stop the villain for good and escape from the wreckage. As they are resting after the final battle, Rorke suddenly appears again, breaks Logan's arm and kidnaps him, announcing his intent to brainwash the latter into killing the other Ghosts. This is patently absurd, for several reasons:
No game in the Call of Duty franchise prior to this has seen an antagonist have a Disney Villain Death, especially to the point that they survived being repeatedly beaten, shot in the center of the chest and left to drown in a wrecked train. Even Soap's injuries from Modern Warfare 2 were serious enough that he required surgery and rest for several days before he was back up, and his wounds never fully healed. Rorke just pops up again and overpowers the player for no reason whatsoever.
Rorke's plan is a complicated Xanatos Gambit involving Logan being brainwashed and planned to kill the other members of the team. This makes little sense considering that Hesh is a member of the Ghosts, and Rorke leaves him alive, despite knowing that they are both Ghosts!
Also, to add insult to injury, this all could be easily averted, since Hesh and Logan perfectly knew that after retaking the LOKI space station, the entire rod armament will be at their disposal ready to be used. If they never got on the train to chase after Roarke, the ghosts from the space station would of been able to just drop a rod strike on top of the train and easily kill Roarke without any risk at all.
Speaking of Ghosts, downloadable content adds killstreaks that allow you to turn into horror movie monsters such as Michael Myers or a Predator, or unleash a horde of aliens on the opposing forces. This is very jarring, considering that the Call of Duty series usually tries to keep a realistic military setting, and saves the fantasy/sci-fi elements like aliens and zombies for secondary game modes.
Elias and three other Ghosts are sent to assassinate General Almagro because he supposedly, "Ordered the death or imprisonment of every US-born citizen," for quite literally no reason whatsoever. This is made even worse, because the only evidence we have of this is Elias saying so, and the antagonist in the game, who works for the Federation, is a US-born citizen. In fact, there are only two Federation citizens in the whole game who actually have a role other than generic mooks to be mowed down: the aforementioned General who is killed less than ten minutes after his introduction and has no lines, and a civilian who they torture and threaten at gunpoint for about five seconds before he's forgotten about. We essentially know nothing about who we're fighting. We never find out their form of government, their goals on taking over America, or generally any idea why they exist in the first place.
The Bad Ending. OK, so Cordis Die burns the world. OK, so the apocalypse virus destroys civilization. OK, so Menendez beat our asses at every turn. That's justifiable. Its our fault for not completing those Strike Force missions and making poor story choices in the earlier levels. That's why its called the Bad Ending. But Frank Woods does NOT die like that, dammit. He simply does not sit there in a wheelchair and passively wait for Menendez to come murder him, especially not after watching Menendez kill yet another innocent American soldier right in front of him. This is FrankWoods we are talking about here. This the man who has had Menendez take away everything and everyone he ever loved. This is the man who's been waiting to kill Menendez for 30+ fuckin' years. And he knows Menendez is coming for him — he even greets Menendez with a "Yeah, I been waitin' for this." — but he still just sits there? At the very least Woods would go 'Yeah, I been waitin' for this... which is why I got a backpack full of C-4 in this wheelchair. See you in hell, asshole!' *BOOM* Instead, we get Woods turning into an apparently senile old man who can't even muster so much as a simple 'Fuck you' to Menendez as he dies. *headdesk*
Its not like they even needed to keep Menendez alive for sequel use or anything - Menendez kills himself in the Bad Ending, shortly after he kills Woods. So they want both characters dead anyway, but still won't give Woods the minimal salvage of 'Well, at least he took the SOB with him'.
Conversely, the best ending has a scene where (if you shoot him in the knees instead of the head during "Time and Fate") Alex Mason himself appears at the Vault and reintroduces himself to his son and Woods. This is handwaved by the character in question mentioning that Woods was a "lousy shot", but no explanation is given for where Alex was for the last 30-plus years, why he only decided to show up after Menendez was captured, and why he never bothered to contact his son during this time period.