The following are real headscratchers. Ever wonder:

-Why you can't find the spy in the Followers or turn off traps in the Glow even though they show up in the Quests section on your Pipboy?
-Why did they cut out so many other quests and npcs?
-Why were the roles of Killian and Gizmo orginally reversed where Killian was the bad guy?
-How come when you speak to Nicole again if you have low intelligence, her floating dialogue is voiced?
-How come Beth and Rutger can recognize you as a member of the Brotherhood in Power Armor, but not Hardened Power Armor?
-If Doc Morbid, Jain, and Darren Hightower are considered evil characters, why does killing them reduce your karma?
-If Doc Morbid removes your eye, how come it is magically replaced if you use the Doctor skill?
-How did the Master reach the Cathedral if he is immobile?
-How come a low intelligence character can speak a perfect english sentence in dialogue with the leader of the Crimson Caravan?
-How come when you search a bookcase, sometimes you bend down as if to pick it up?
-How come you can't reach Sasha the dog outside the Cathedral?
-When Neal kills the Skulz ganger that hit Trish, why do his death throws resemble that of getting critically hit by a burst fire weapon rather than a single shot?
-Why do you gain karma from killing most of the ghouls in Necropolis?
-Why does Synthia get mad at you if you kill the crazed raider despite the fact that he threatened her life?
-Why is Power Armor and its hardened variety much lighter in the second game?
-How did Frank Horrigan get into the Brotherhood bunker, Vault 13, or the main entrance hall of the oil rig?
-How come you can't prove your story about talking Deathclaws to Tandi even if accompanied by Goris?
-How come a low intelligence Chosen One can speak much better broken english than a low intelligence vault dweller?
-How come children were removed from the electronic store bought versions of the first game?
-How come a low intelligence Chosen one can speak perfect unbroken english at the bridgekeeper special encounter?
-How is is possible that Marcus and Frank Horrigan can speak normally unlike other super mutants at the time?
-How come Marcus claims that mutants aren't sterile despite Vree's report?
-If all traces of Dick Richardson are erased from history, why do the Eastern coast of the Brotherhood of Steel remember him? And why is the term 'President' still used even in NCR and the Enclave?
-Why do the residents of Vault City treat all outsiders with contempt despite living outside the vault?
-How come a low intelligence male can still box, but not a female?
-How come children are immortal in 3 and New Vegas?
-How come during Trouble On The Homefront you get referred to as 'young man' even if female?
-How come if you blow up the citadel, the initiate refers to you as him even if female?
-Why do so many characters in 3 and New Vegas have the same voice actor?
-How come weapons no longer have a Strength requirement in 3?
-How come in 3 and New Vegas, you now need training to wear Power Armor?
-Why did they change the location of the setting between the first two games and 3?
-How come traits don't appear in 3?
-How come Nuka Cola restores your health in 3 and NV while it had no effect in 1 and 2?
-How come ammo in 3 has no weight?
-Why are Reavers, Overlords, and swampfolk so tough and deal damage that can't be resisted?
-How come the Brotherhood wants to wipe out ghouls despite them not being as dangerous as the Super Mutants?
-How was Harold's heart moved into a cave, yet he is still breathing?
-How come weapons and armor in 3 and NV have durability?
-How did Moira become a ghoul so quickly if you blow up the town?
-If they are marked as hostile on your compass, how come the convicts at the Nevada Gas Station do not attack on sight?
-If Boone is hostile towards the Legion and vice versa, why isn't Veronica hostile towards NCR and vice versa?
-Why would Arcade be in trouble from NCR and the Brotherhood despite not officially being a member of the Enclave?
-Why is there so much unradiated water in the Mojave compared to everywhere else throughout the franchise?
-Where did the lettuce and tomatoes come from in the sprite for Desert Salad if neither were even an ingredient?
-Why are food items you get from Them's Good Eatin forbidden by the Legion and why don't they reduce your starvation level in Hardcore mode?
-Why do they still use caps for trade in the Mojave despite the fact that NCR has it's own money at the time of 2 and was the main currency then?
-Why does the Courier know that the Weathers' went to the Freeside fort if they never told him/her?
-Why doesn't Christine react if you play any of the holotapes she made in Old World Blues?
-How come certain recipes unlocked by Vigilant Recycler require less of a Science skill than is needed to qualify for the perk?
-Why doesn't Trigger Discipline and Fast Shot affect automatic weapons?

If I come up with any more, I'll post them.

-Why did they cut out so many other quests and npcs?
Not enough time to realize all of their ideas - a common occurrence in game development.

-How did the Master reach the Cathedral if he is immobile?
He didn't change all at once. Plus he had an army and a cult by then.

-How come you can't prove your story about talking Deathclaws to Tandi even if accompanied by Goris?
He doesn't want to reveal himself.

-How come children were removed from the electronic store bought versions of the first game?
-How come children are immortal in 3 and New Vegas?
Violence against children is a touchy subject in most places, and most people can enjoy the games perfectly fine without it.

-How is is possible that Marcus and Frank Horrigan can speak normally unlike other super mutants at the time?
Some mutants retain their intelligence, especially if they weren't already irradiated. This is why the Master wanted vault dwellers untainted by the outside world.

-How come Marcus claims that mutants aren't sterile despite Vree's report?
retconned

-If all traces of Dick Richardson are erased from history, why do the Eastern coast of the Brotherhood of Steel remember him? And why is the term 'President' still used even in NCR and the Enclave?
It would take some time for him to be completely forgotten, but the office of president doesn't vanish with him.

-Why do the residents of Vault City treat all outsiders with contempt despite living outside the vault?
They consider themselves more advanced and civilized, and they're not entirely wrong.

-Why do so many characters in 3 and New Vegas have the same voice actor?
It's expensive, and they already licensed a bunch of music.

-Why did they change the location of the setting between the first two games and 3?
New developers wisely chose to do their own thing so they wouldn't have to worry about continuity with the original setting. New Vegas was made by most of the old crew, so they returned to the original setting to explore concepts intended for their Fallout 3 which was cancelled.

-If Boone is hostile towards the Legion and vice versa, why isn't Veronica hostile towards NCR and vice versa?
Boone has a personal vendetta against the Legion, and his first recon beret makes him very recognizable as NCR. Veronica is used to going incognito on the surface, and she has an entire character arc about wanting the Brotherhood to adapt and modernize, which includes ending their feud with NCR.

-Why would Arcade be in trouble from NCR and the Brotherhood despite not officially being a member of the Enclave?
Enclave basically made enemies of everyone, so anyone associated with them is going to be distrusted.

-Why is there so much unradiated water in the Mojave compared to everywhere else throughout the franchise?
House shot down almost all of the missiles that would have struck the Mojave area, so there is less radiation.

-Why do they still use caps for trade in the Mojave despite the fact that NCR has it's own money at the time of 2 and was the main currency then?
With House and the Legion present, NCR has been unable to annex the Mojave.

-Why doesn't Christine react if you play any of the holotapes she made in Old World Blues?
OWB was made after DM. For technical reasons, one dlc cannot modify another.

-Why doesn't Trigger Discipline and Fast Shot affect automatic weapons?
Firing rate of fully automatic weapons has nothing to do with how quickly you pull the trigger.

-Why doesn't Eldridge get mad at your companions if they go into the back area of his store?
-Why don't Hightower's guards care if they see your followers at night?
-How is it possible that a Low Intelligence Courier can still make speech checks while the Vault Dweller of Chosen One can't? And why can a Lone Wanderer with low intelligence still communicate in a way that anyone with normal intelligence can?
-Why do you lose karma for killing certain people who attack you completely unprovoked, such as homeless people or addicts?
-How come certain evil characters in the first two games give you a positive reaction when you first speak to them even if you are good?
-If drugs are forbidden in Vault City, why does Lynette have Mentats in her inventory?
-Why do you lose karma from pickpocketing your fellow tribesmen even if you don't actually steal anything?
-How come in Fallout 3, the Gatling Laser is now catergorized as a Big Gun instead of an Energy Weapons?
-How come in New Vegas, Flamers and Heavy Incinerators are now categorized as Energy Weapons?
-If slavers turn hostile if you are a ranger, why doesn't Metzger?