1. Watch very closely when Neo starts fighting the Agent in the subway. When the Agent punches the wall above Neo, watch very closely. When Neo's back is to the camera, look at the pillar that the agent punches, in the exact location of where he punches. There you see break away marks!!!
2. (Hint) When they show the "Matrix Code" it is just a combination of numbers, and reversed Japanese characers.
3. (confirmation) Yes i think it's a error when they show the pillars when the bomb is going off, simply because if a bomb was going downward, it'z blast would be going down, throuh the floor, but instead, the bomb blast is level. It is a simple fact of what us "Living" Humans call gravity