Continuity mistake: In the subway fight scene, Neo is thrown to the floor and wipes blood from his mouth on his hand. It then cuts back to Agent Smith. When it cuts back to Neo, he assumes a fighting stance and you can see that there is no blood on either side of his hands.
Continuity mistake: In the subway fight sequence between Neo and Smith, you see Smith swing his right fist toward Neo. When the camera cuts to a closer shot, Smith is swinging his left fist toward Neo.
Continuity mistake: In the "Deja vu" scene, Neo uses a CZ99 pistol to shoot through the wall at the police officer, but when Agent Smith bursts through the wall and grabs him, Neo is holding a Glock 17.
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 ★