In a different situations with longtime running game server mobs just won't naturally spawns at world (Overworld/Nether/End).

It's can be fixed only with server restart, but not for long time - spawn rate brokes again when some count of players will connect to game, play some time and disconnect.

Steps to reproduce:

1. Run multiplayer game;
2. Play some time with other players;
3. Do a disconnect from server;
4. ...

Here's an example from my dragon battle game (in russian, but it's not important). There's no any hostile mobs (and Endermans) was spawned during a gameplay (excl. Ender Dragon) 

Gameplay on YouTube - http://www.youtube.com/watch?v=QoXbCUA4nRk