Situations like that may occur. Remember my story about losing 2-1 in the playoffs last year. Look at the big picture though. What kind of ref were they the rest of the game? If they are consistently missing calls or seem to be one sided, request your assigner not use them at your games anymore. I have done that when I felt a ref was not objective. In the offsides situation, it only applies to the person who receives the ball. Once they receive the ball anybody who is beyond the ball is now offsides and if the ball is passed to them they are offsides. Not knowing the full scope of the situation, I'm not sure how to make the call.
What do you do? Live with it and remember to carry your rule book with you and let your assigner know. If it is your assigner, let them know at the league office. Losing your temper and yelling at the ref is just going to make matters worse. You are not going to change his/her mind by screaming at them. If anything, they are probably going to hate you that much more. All yelling and screaming does is makes you lose your voice.
