Steps to reproduce:

1. Start a server. It helps if you configure it with /gamerule doMobSpawning false and kill any existing entities.
2. Locate a chunk at the edge of the always-loaded "spawn chunks".
   • If you /setworldspawn -112 4 184, chunk <-4,19> is such a chunk.
3. Place fire (on netherrack) at the edge of the chunk, or one block in.
   • Using the example above, -116 Y 319 and -116 Y 318 work.
4. Place an entity in the chunk just past the spawn chunk.
   • In the example above, that would be somewhere in the <-4,20> chunk.
5. Log all players out of the server.
6. Wait a while; I suspect we're waiting for the fire to try to spread.
7. In the server console, /testfor @e. You'll likely see it somehow found your one entity multiple times! Using /entitydata @e {} to dump the entity data will prove it's seeing an identical entity.

A player logging into the server causes the duplicated entities to be cleaned up. OTOH, leaving the server running without players for long enough will use more and more resources and eventually crash.

The attached world.zip is a world set up as described here.