I haven't watched the replay again, someone said he put his hands behind his back, ref's do that to signal they have given nothing, in which case he didn't play the advantage. As for playing the advantage, posession doesn't equal advantage, someone can foul, other guy can still have the ball and the ref see's if anything useful happens, if he runs forward and loses it 2 seconds later, there was no advantage and he'd pull it back.
As I said before, its a little difficult, if a player runs away from the ball, he hasn't had an advantage, but neither was stopped from having an advantage, thats the thing, the advantage is allowed but if someone stops that player/play from happening thats the point he'd give a freekick unless it was quite a while later.
Gomez lost the advantage, but really of his own fault, I really don't know if the ref takes into account a players stupidity or not. Its an odd one, but its all mute if he did put his hands behind his back, indicating no freekick, no advantage, nothing.
Likewise, NO ONE but the linesman knows what he flagged for, you can flag for anything, infact when you see the ear piece fail you've seen linesman flag to get the ref to come speak to them before. He may have said penalty but the earpiece didn't actually transmit so after the goal was given he got the ref's attention said it was a penalty and the ref just left it as is, if thats what happened he could have pulled it back and given the penalty, but also sent Kaboul off, there was a slim chance of them not scoring, or leaving as is, definate goal, but Kaboul still on, its kind of evens out either way and leaving as is was less of a **** storm at that point.
Who knows, no one till the ref/linesman say what happened exactly. HOpefully the FA will investigate it and both will have to say exactly what happened and why.