The Jones play was not a penalty, it was close but the defender played the ball first. If Jones was one step faster he might have got there first. And if Stern was there he would have been nowhere near the ball or defender.
from the tv replays our goal was definitely offside and theirs wasn't. The man who trap the ball from the cross was marginally offside and there were two others much more offside that may or may not have been considered to be interfering with the play. But all 3 were offside.
Also that is the new rule where the linesman waits until the player touches the ball before flag goes up. If he doesn't touch the ball and turns around and runs back and doesn't interfere with play they don't bother blowing the whistle.