Here is what happened: During the first 10 minutes of the game a goal is scored but right afterward, (during celebration of the goal), to everyone’s surprise, the center referee stops play and goes to talk with the side referee. No one knew why at the time. Players that were in the area of discussion said that the center ref asked the side ref why he had put his flag up and then quickly down before the goal was scored. The side ref told the center referee that he did not mean to put up his flag and that it was a goal. The center ref says well you did put up your flag and so I blew my whistle and so whether you meant to put your flag up or not, you did, and so since I therefore blew my whistle I can not call it a goal. The side ref then said well it was a goal I made an error and I clearly saw that the goal scorer was behind the defender and it was a goal. But again the center ref said well I can’t count it as a goal. So he calls it no goal and does a drop ball. Now I must add that no one heard the whistle be blown and play continued during the goal being scored, no players stopped playing. What is the rule on this? How can an obvious goal not be counted just because the side ref accidently puts up his flag for a brief moment? And then the side ref says it is a goal. The center ref even came over to the head coach during half time to say that he knew that it was a goal but was sorry that he could not count it but under the circumstances he could not. By the way, this goal ended up being very important to the out come of the game. It was the only goal scored and made the difference between a tie and a win! And the points were needed, now its the difference between 1st & 2nd place in the bracket! Bummer! Thank you for your explanation and can anything be done at this point? Can a protest maybe correct this?

USSF answer (October 31, 2011):
The referee acted correctly only if in fact he had blown the whistle upon seeing the AR’s flag go up. He apparently reacted (albeit inaudibly) to his assistant referee’s flag and stopped play for whatever the flag may have meant — offside, foul, etc. The fact that the AR then lowered the flag does not make any difference in the outcome; the referee’s decision was made and the whistle was blown (even if inaudibly). Play stops when the referee decides it has stopped. Anything that happens after the decision to stop play has been made does not change the fact of the stoppage.

No, the referee has not misapplied the Laws or called something counter to the Laws, so we doubt that any protest would be allowed. If the referee included full details in the match report perhaps the competition authority will have pity.