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NSFW - This trivia is considered "Not Safe for Work" - Click to Reveal
At the Farris Halstead Library train station in the Loop, if you follow the tracks to the east, you will discover a junction where opposing straight tracks from the north and south intersect with the eastward tracks. These eastward straight tracks are unusual in that they appear to continue and stop before the edge of the elevated platform with no bumpers to mark the end of it, appearing unfinished, although it should be noted that no trains traveling eastward will actually go down these straight tracks all the way due to the curved transition tracks guiding them away. In the real-life Loop in Chicago, this spot would be located at the junction right after the Harold Washington Library train station, which unlike its depiction in Watch Dogs has no straight tracks continuing after the curved tracks at all.

The day before Watch Dogs' release in May of 2014, an anonymous 4chan user claiming to have worked on the game posted insight on the game's development and their experience working with Ubisoft Montreal, including details on how the train tracks worked in earlier builds of the game:

"Earlier when we were just working on world buildings etc, Montreal said we need to create a path for the L-train so that's what they did, but they put fucking 90 degree turns on the tracks! So I asked them for time/resources to fix this, they respond "we don't see your issue."

So I went ahead and sent them a video of this, showing how retarded a train running at 80mp/h looks when turning 90 degrees, they tell me "We see your issue but it's too late, maybe we'll patch this later." This was back in October [2013], before the delay announcement etc although you can probably still see in the game tracks marks left of that, which we missed cleaning up. In the October demo that was shown with the train if it went any further you'd see the 90 degree turns."

In 2020, an early build of the game dated to September 21st, 2013 was dumped online by YouTuber JustAnyone, but it's currently unknown if this mistake existed in this build.
Contributed by MehDeletingLater
In the mission shown during the gameplay demo shown at E3 2012, Aiden is shown killing Joseph Demarco. The mission was changed prior to release, and instead killing Demarco, Spoiler:Aiden now has to kill a hacker, Defalt.
Contributed by ClaudX
The town Pawnee is based on the real life town of the same name. However, the game portrays Pawnee as being located right outside of Chicago, when it is actually located near central Illinois.
Contributed by ClaudX
While modding the PC version, a user by the name of "The Worse" found almost all of the shaders and graphical improvements present in the 2012 and 2013 trailers for the game. It's possible that the PC version's graphics were downgraded so that it would not make the PlayStation 4 and Xbox One versions look drastically inferior by comparison.
Contributed by Boyobmas
In some randomly generated vehicles, there is a chance that the keys will have a keychain of what appears to be a My Little Pony character dressed as Aiden.
Contributed by Psychospacecow
Inside Iraq's hideout are a number of arcade machines featuring the logo of Far Cry 3: Blood Dragon.
Contributed by Dazz
During one of the optional Privacy Invasions, the player can see an emotional discussion between a stage II cancer patient and a woman working two jobs. The conversation and characters themselves are a direct reference to the TV series Breaking Bad.
Contributed by Dazz
Graffiti can be found around the city that resembles the Slenderman.
Contributed by Boyobmas
Aisha Tyler (famous for her role of Lana Kane in the animated comedy Archer) makes a cameo appearance as herself in the role of a citizen NPC. She can be discovered while exploring Chicago, but can be easily found in Connely Square just outside of the Willis Tower in the mission "A Wrench in the Works". She is also the subject of a Privacy Invasion activity.
Contributed by totallytman
Every sign in the game reveals a famous meme or quote when hacked.
Contributed by Tuli0hWut
Inside Nicole Pearce's house is a Rayman Raving Rabbid toy that laughs when hacked.
Contributed by Psychospacecow
During one of the gameplay trailers. a man can be seen dancing in his apartment. His information states he is a video game store clerk and has legally changed his name to "Eddie Kenway". This suggests the man is a fan of Assassin's Creed IV: Black Flag, as Edward Kenway is the name of the main protagonist in that game.
Contributed by Boyobmas
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T-Bone is shown to own both Assassin's Creed II and Far Cry 3, two other Ubisoft titles.
Contributed by Boyobmas
One of the camera feeds that the player can hack into shows a father watching his son play a video game. The father is mocking how the assassin in the game talks to the people he kills. This is a reference to the Assassin's Creed series (also developed by Ubisoft), in which the protagonists talk to the people they kill before they die.
Contributed by Boyobmas