
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)
Chosen answer: The pills are the Matrix representations of computer programs. The red pill contains code designed to disrupt Neo's input/output signals, so that Morpheus' team can pinpoint his physical location in the real world. Once located, a signal of unspecified type is sent from their ship, which presumably serves to wake Neo up.
Tailkinker ★