by young bees, you mean brood?
is there brood in the bottom also?
a couple of things could have happened.
the queen might be small enough to go through.
if you moved frames, did you put them above the excluder? if so, and there were eggs on that frame, they may have made another queen.
if you have two queens, you can make a split and have another hive. if the queen is moving up and laying, you might as well take out that excluder. all it will do is trap drones.
you can take out the excluder and just let them do what they want to do. a two queen hive is not a bad thing.
you can put the excluder above and put honey supers on top.
whatever has happened, it doesn't sound like the end of the world. you just have to figure it out and decide how you want to handle it.