I hatched 5 eggs...but only have 3 flying. What happened to the other 2?

They fly as flocks and they come and go. You have to watch your island for a long period of time to see them all. The geese fly in V-formation across the island. The seagulls tend to flock around the Hangar. The parrots tend to fly around the Chapel. The Starlings tend to flock around the Mountain Chateau. But they really move all around. The more birds you have, the easier time you will to find them. To see the total number of birds you have, tap on the Aviary and the number is next to the bird symbol in the upper right corner.