Steps to resolve:
1. Find the duplicate dragon on your main island and place the dragon in Dragon Stable.
2. Visit the Arctic Isles
3. Tap the habitat your "copy" dragon used to live.
4. The game will close.
5. Restart the app. The "copy" dragon will be gone.
9-14-16- Edit (KP)
I just hatched ****er Whale on the Arctic Isle and fed it to level 3. Hatching ****er Whale took me over the 3,000 points on the Leaderboard and I received Tanuki
Went back to the main islands, pottered about doing bits and pieces including putting Tanuki on the nest, went back to the Arctic Isle and ****er Whale is no longer there. Just vanished into thin air.
I have never had this happen before.
iOS version 9.3, iPad Air 2
I have force closed the game, restarted the device but have not yet uninstalled/reinstalled. I have also emailed Support.