This is a very annoying and infuriating bug. I enter the end FOR THE FIRST TIME. After entering I go and search for the ender dragon to fight it. I die and respawn back in the overworld. I go back to the end and see that the ender dragon is no where to be found.  I search the entire island I don't see it. Then I go to the exit portal and it is lit but no dragon egg. This happened in various of my survival world where I worked really hard. I have tested this in varios other worlds and the same problem persists. Later, I decide to look for the portal to go to the end city. it is no where to be found. I search everywhere and I can not find it. This is very infuriating as I can not get the dragon egg nor can I get to the end city. I tried re fighting the end dragon by spawning it again but even after defeating it, the problem still persists. To make things worse, once I go back to the overworld, there is a ender dragon that has destroyed my hard worked base at my spawnpoint. Please fix this as it has cost my many hours of hard work.

Things to do to recreate this situation: 

1. Find the stronghold. 
2. Set a bed spawnpoint in the dungeon
3. Light up the portal.
4. Enter the portal.
5. Make sure that the ender dragon boss bar is visible.
6. Die to the end dragon. 
7. Spawn back in the dungeon.
8. Re enter the portal.
9. No end dragon nor end city portal.
10. Enter the exit portal of the end.
11. Spawn back in the overworld.
12. Go to world spawn point (The place where you first spawn when you create a new world. Not the manual spawnpoint created by sleeping in a bed)
13. You will see the ender dragon flying around in the overworld, destroying the land. 

This has been a bug since the starting of 1.5 and it is still unresolved.