I can't argue with you GRHinPorts because we simply can not see, it seems to me that Senna was half way alongside, until we see an external replay of the incident, neither of us know!
On a separate occasion, Vettel appears to overtake a Toro Rosso under yellows.
[youtube]MZHaBuaA9oQ[/youtube]
Vettel definitely overtook before the green electronic flag board on the left, I believe the rule is that a driver has to be past the electronic flag board before overtaking?
Correct me if I am wrong!?!?
It's been talked to death on other forums, so I'm not going to go into too much detail, but he was actually green-flagged by a marshall post in between the two lights.

Although it's very grainy (as all the footage is really, is this 2012!?), onboard shots from Alonso show that if it was a yellow flag, it would be very easily distinguishable. As it's not, and there was no reason for a blue flag, it must be a green flag (powers of deduction ftw!).
Not every marshall post has a light, but every flag signal still counts; they have precedence over any electronic signal.
Manual flags are just not translated to the steering wheel (how could they), but he overtook under the green flag of
the marshall post near the pit exit.