OR, the Wbro's and producers didnt think of the common sense of it. Or did realize it and left it alone, needing it to happen for a giant part of the plot for Revolutions, knowing only .1% of the people watching would catch it.
When you start making up an excuse/reason for EVERYTHING, you start making up your own storyline at the same time. Im sure if we all had the chance to grill the Wbro's at the same time, we can back them into a corner where they wouldnt have some answers. Like maybe THIS one.
Now for this particular scenario, theres no reason why people watching the Matrix COULDNT see the conversion when Smith multiplied himself onto someone else. In the BIGGEST Smith fight seen, were they watching Neo kick the crap outve ONE Smith, Uncle Tom, Aunt Louise , Granny and a Hundred other people? No.
The only possible THEORY to this is people on board werent watching the matrix screens as Smith injected and turned... and called there without looking. Maybe when the first dude went up, he started talking to everyone about the events. (OR they all started scrambling to put the Oracle's message on disk? another weird theory)
If they did see it happen, Id doubt theyd call to let him come through. Unless they wanted to kick the crap outve a "real life" Smith. Maybe they were disapointed when he came back as Bane and didnt know he was acting strange.. (yea right) Im sure they wouldve locked him up for a long while to see if anything happend to him mentally.
Since they didnt explain it, its just a hole for us to fill in with guesses...
Id say its a hole they overlooked when making the film.