Continuity mistake: In the interrogation room. Mr. Smith has a green file with him with Neo data accumulated. Smith opens the file and lifts up some pages without turning them fully over. In the very next shot there are suddenly multiple pages to his left which have already been turned over. (00:16:50)
Continuity mistake: When Neo first meets Morpheus, Morpheus extends his right hand with his other hand behind his back. Next shot shows Morpheus with his left hand at his side, and when he withdraws his hand, it is back behind his back. Talk about fast hands! (00:24:55)
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 ★