Character mistake: When Morpheus is explaining to Neo the reason the Matrix exists, he states that a human being gives off 25,000 BTUs of body heat to help power it - this is just not true. Even human beings that are running a marathon can't give off that much heat, and the humans in the Matrix are all lying down, not moving.
The Matrix (1999)
1 character mistake - chronological order
Directed by: Lana Wachowski, Lilly Wachowski
Starring: Keanu Reeves, Laurence Fishburne, Hugo Weaving, Joe Pantoliano, Carrie-Anne Moss, Gloria Foster
Continuity mistake: When Neo is out on the scaffolding and loses his phone, the first shot down is of an empty street, in the shot of the phone falling the street is filled with people and a big parade, then it cuts to a wider shot and the people have vanished again. (00:15:55)
Morpheus: You take the blue pill - the story ends, you wake up in your bed and believe whatever you want to believe. You take the red pill - you stay in Wonderland and I show you how deep the rabbit-hole goes.
Trivia: It's been said that Neo is an anagram for "one". I think it's more important to realise that Neo means "new". His real name is Thomas Anderson. He is called Thomas at the beginning of the movie, when he doubts the truth -- that the world as he knows it is not real. Thomas is the "doubting" disciple in the Bible. Moreover, Anderson means "son of man". Hence, Neo Anderson is the New Son of Man. The biblical references go on and on... Trinity, Nebucadnezzar (the name of the ship -- in fact, the name plate on the ship makes reference to a verse in Mark chapter 3), Zion... So not only is Neo "the One", he has gone from being the doubter to the new son of man.
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Answer: He doesn't know that he's plugged into a giant computer and that most of humanity is a power source for robots. He's merely aware that there is something wrong with life in general, something odd that he can't quite explain.
Gary O'Reilly