In The Matrix Reloaded, there's a scene where Bane (the one who gets taken over by Smith) and some other guy (don't remember his name) are running from the Agents with a message from the Oracle in an envelope. Bane hands the envelope to the other guy and says "The only thing that matters is this". The other guys puts it in his pocket and then jacks out of the Matrix. Later on, the message from the Oracle is handed to Neo. This seems to imply that the item in his pocket was taken with him to the real world when he left the Matrix. Obviously, this is absurd. So how did the message get out?
Note that I'm looking for an in-universe explanation for this and not wild speculation