When Smith assimilated Bane, why didn't the operators in Zion notice the code change (which I assume one would have to be watching the screens)? I would guess each individual has their own unique code, as operators seem to read where certain people are at any given time.
At the time that Smith assimilated Bane, all the Zion hoverships had been ordered to return to Zion by Commander Lock. Only one ship, the Caduceus, remained at broadcast level, and only because its captain (Ballard) agreed to defy Commander Lock's order and wait for a message from the Oracle. Consequently, only one operator could have been monitoring the Matrix when Smith assimilated Bane. Furthermore, that operator wouldn't have recognized Smith's code because Smith was no longer an Agent.1 The operator would have had a small window of time to notice something weird happening to Bane between the start of Bane's assimilation until Bane-Smith jacked out, but that window lasted only about thirty seconds.2 The operator evidently was not paying attention to the Matrix feed of Bane during that small window, otherwise he would have ended the phone call before Bane-Smith could jack out. There are several possible reasons why the operator was not paying attention:
- The operator was probably helping Malachi (the operative who jacked out just before Bane) remove his head jack in the real world. Someone in the real world usually helps a person remove his head jack (e.g. Tank helped Neo and Dozer helped Morpheus remove their head jacks after the jump training program in The Matrix). The operator would have been the only one able to help Malachi if all the other crew members were still jacked into the Matrix.
- The operator may have been busy helping other crew members in the Matrix at the time (e.g. finding an exit, giving directions to run away from an Agent, loading equipment, etc.).
- The operator may have been watching for Sentinels in the real world. One of the captains at the Crisis Meeting mentioned that the Sentinels had recently made it more difficult to hack into the Matrix, so Sentinels would have been a serious threat.
1 Link, the operator of Morpheus' hovership, did not recognize Smith's code earlier in the film, when Smith appeared at the Crisis Meeting:
Morpheus: What happened back there, Link?
Link: I can’t figure it out, sir. Agents just came out of nowhere. And then the code got all weird. Encryption I’ve never seen.
The Matrix Reloaded transcript (source)
2 See the window of time for yourself: