I disagree Rich... well sort of.

On your CREW - yes, you are right.

This sitch is obviously not a "crew" as much as it is a hodgepodge of officials working underclassmen games. The OP is a 1st year guy. I don't think it's entirely unexpected that a 1st year guy may feel wrong about having his flags waived off (especially in a case like this, where the overbearing R didn't even explain to him why and simply played Referee God and waived it off himself). This is not a problem with the "crew" that he might feel this way in this sitch. OP will learn as he gains experience that having a flag waived off is not an offense, and hopefully he will work more often with Referees that choose to guide and mentor, instead of run roughshod over his "crew" with no explanations.