After coaching for the last 6 years I have plenty of stories for this topic!
In an Atom house-league game (9-10 year olds), we were up 2-1 with 2 minutes left in the game when our goalie dropped his stick. Our defenseman picked it up for him and handed it to him and the ref immediately blew the play dead and called a penalty on him for holding two sticks at once. I tried to tell him that it only applies if the player tries to play with both sticks, which did not happen, but of course he wouldn't have any of it. I thought maybe I had the rule wrong, but later on I confirmed it with the head referee for our region that as long as you do not participate in the play with both sticks, it's not a penalty.
In a Novice A semi-final tournament game (7-8 year olds) the referee called a penalty on us in the third period. I started worrying about which players to get on the ice and giving them a couple of instructions and did not pay attention to the referee bringing our player to the box... The play starts, we're 5 on 4, and about 30 seconds into the penalty the referee blows the whistle and skates over to our bench and tells us that our player was not in the penalty box! I was confused and looked over to the penalty box and saw it was empty... When the referee called the penalty the other ref did not escort our player to the box, so he just came back to the bench. Of course at this point the other teams coach is hollering that the ref needs to give us another penalty now.
The referee tried to tell me he was going to give us a 2nd penalty now. I politely told him that it was HIS job and his responsibility to make sure that the player gets put into the box when a penalty is called, not mine. The problem now is that he does not remember who was supposed to get the penalty, so he tells me "Fine, I won't give you another penalty but your #10 has to go in the box", with #10 of course being our best defenseman.
In that same game, we are on a powerplay and the play starts, except the timekeeper forgot to start the other team's penalty timer. 20 seconds later, as we break-out on a 2 on 1, the referee notices the timer and BLOWS THE PLAY DEAD, instead of just letting them play on and either fix it at the next whistle or to just have the timekeeper tell the player in the box what time to get out at and ignore the timer. So they blow the play dead, take the 20 seconds off the other team's penalty, and have a face-off at center ice. Bravo.
I know in Novice you always have the younger beginner referee's, but it was the semi-finals of a tournament and it was 2 adult referee's working the game. Luckily we ended up winning the game anyways.