Illegal sub?? (New Ref)

[Cole4088]

So, I'm new to the officiating world. I had a partner today that has been doing it for 3 years and is a little shaky. This is a middle school boys game. We resumed play with a throw in Team A only has 4 players AFTER the throw in. They start yelling we only have four players. So, a player runs off the bench and play continues. I look at my partner he doesn't look concerned. I searched the case book.. Can't find anything..