AFAIK, the siege bug is that the attackers have not won at this point, since the flag is already down. Basically, it just delays the attacker victory, not really changing the outcome.
It's a really annoying bug that often cost's a lot of people a multi, as said sometimes the flag is not at the very bottom yet defenders still lose! Really hope they sort it out or at-least post saying if its a bug or not. 
you need to play siege more i guess, the flag is ALWAYS at the bottom when this happens. you can even predict when the flag is bugged. the pole is sometimes just a little bit deeper in the ground
