Sounds like you were technically out of line in that you failed to stop at a stop sign, but in terms of practical impact it really makes no difference. I'd liken it to a pedestrian crossing where one pedestrian pressed the button to get the signal to cross, then crossed anyway only for the light to change as they completed their crossing. Technically you're required to wait until the light turns green again but it's easy to see why an operator of a relatively slow vehicle that can't be readily identified would just go through regardless.
Doing 80mph in a 70-zone on road where you've got three lanes that are totally empty in the middle of the night is technically illegal but it's hard to see very many reasons why it's a big deal.