When Morpheus traps one of the Twin's arm in a door and shoots it, why doesn't the Twin Ghost and pass through the door? Instead the other Twin has to threaten Trinity so Morpheus will open the door.
If Smith is no longer working for the system and appears to be working as a free agent, why does he help the Matrix octopus bots take out the ships from Xion? For that matter, why do the bots leave him alive (he's the only one, apparently)?
They never did really explain where Smith suddenly got the ability to act virus-like, either...