When you move the Spawnpoint with the /setworldspawn and then go in to the Nether and exit it again, the spawnpoint gets set to 0,0. It happens on servers and in singleplayer. If you disconnect and join a server it is not happening.
Also happens when you just create a new World and go to the nether and back. The spawnpoint will then be changed to 0,0.
Happens also in 15w36d.
Related issues
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I just created a new world and checked the spawn with the compass. it was where i spawned. Then i flew to another location and run /setworldspawn. After that i checked spawn again with the compass and it was at the new location. When i now go to the nether and back my compass is not pointing at the new spawn point, it is pointing at 0,0.

Duplicate of MC-679
Cannot confirm for 15w37a
How did you noticed that the spawnpoint was set to 0,0?
And did you maybe overwrite the world spawn point with the
/spawnpoint
command?