There are some "odd" things in the game story, like:
A) Rogue says to V (if you go to the Afterlife) that he/she works alone because after the job with Dex went south, people don't trust him/her. But then, even before knowing about Silverhand, she hires you to do some gig for her (depending on what order you're playing the game). It's at least strange.
"You're not trustworthy, so nobody will work with you, but, you know what, if you want a job, you're hired"
B) I find very odd how V invades Eurodyne mansion, start using his guitar to play Samurai songs, and when confronted, tells him he/she is his former band member (which only mistreated him, btw), talk about the engram (which is obvious to the player and for V, but should sound like a totally insane technobabble to an artist), and suddenly he is very friendly and talk openly about the past.
In the other hand, nobody, except Eurodyne knows that V is (something like) Silverhand. This one is not "wrong", but it's very strange.
"You invade my property, but because you allegedly is Silverhand, we're friends now, mate"
C) Saburo died strangled by his own son, but curiously nobody checked his corpse, saw any kind of mark, and everyone magically accepts that he was poisoned. Not even Smasher (security boss) took a careful look into Saburo's body.
In the other hand, when LW killed her "love interest", when V enter the room, as soon as he/she sees the corpse, there's an option where he/she automatically shouts something like: "You strangled him! How dare you?"
"My boss, the most powerful man for decades, just drop dead with clear marks of strangling, but it was poisoning, of course"
D) V and Jackie were clearly seen by Trauma Team, and Arasaka Security, that shoots at them, and that makes them jump from Arasaka Skyscraper, but, strangely enough, nobody recognizes him/her as a former employee (if you play corpo), nor anyone cared to record even a glimpse of V's and Jackie's face before jumping from the roof. A security system that didn't care to record V's and Jackie's face (is that right?).
So when you go by Arasaka Tower, nothing happens, nothing at all, even Hanako doesn't recognize you, she know about you because Takemura talked to her.
Not only nobody recognizes you and Jackie, but there is no signs that someone in Arasaka is trying to investigate Saburo's death, except for Takemura. Not even Hanako - which was a beloved daughter and the feeling, as it was said, was mutual.
Guard 1: "Isn't that the guy who we saw fleeing from Arasaka tower after the boss died?"
Guard 2: "Are you kidding me? That guy was wearing a tuxedo, this one is with a golden cowboy hat, red hobo jacket, green sleevless shirt, blue skirt, and purple high heels, jumping around like a crazy guy testing new legs."
Guard 1: "Yeah, putting it like that... pfff... what am I thinking? Jesus...."
E) Nomads rob a tank from Militech. They send an army to recover it. They fight, and change their location by 1000 meters.
Militech: "That's it folks, I guess we'll never know where they are know, even if they have a giant camp outside Night City, and are hiding a freaking gigantic tank, it's impossible to know their location. No merc, spy or sattelite could find them, nope, better give up now"
That's why Arasaka is always messing with them.
Well, that's the ones I could think now.
