The ender dragon will respawn without player intervention in pre-1.9 worlds where the dragon has already been killed. To reproduce:
1. Create new world in 1.8.9, enter the end and kill the dragon. Do not leave the end.
2. Open that world in the latest snapshot, save and quit to title.
3. Open that world in the latest snapshot, observe how the dragon respawned and created a new (unfilled) exit portal.
Looking at how level.dat changes over these steps leads me to believe this issue is related to, or possibly even caused by the fix of,
Attached are a screenshot depicting the end exit portal situation after step 3 and 3 screenshots showing the level.dat structure after each of the 3 steps.