Where did this dragon skeleton come from?

Solution 1:

It's a bug. Sometimes when you kill some things it will pop up near where you killed it. Sometimes you will see it fall out of the sky.

This is fixed in the Unofficial Skyrim Patch, which you can download through Steam.

Solution 2:

Not sure about the zone stuff. But I watched a dragon fly around picking fights with everyone before getting killed by a couple of mammoths. Of course I sniped it a couple of times and took the soul ;)

Solution 3:

Please note that bodies will lie permanently on the ground, or at least for a very long time. When I return back to the first city I was in I saw the bodies I killed in the first minutes I played Skyrim.

There are quite some possibilities for this case:

1. You have fought the Dragon in the past.

2. Some NPCs have fought the Dragon in the past.

3. Some event in the dungeon causes the body to be there, to denote people have fought outside.

4. The Dragon body was there already, from the beginning of the game.
   Highly unlikely, though... Because it would then be part of the story.

5. As Zenonv4 mentioned, it could be that nearby zones are emulated.
   Highly unlikely, though... Because that would have quite some impact on the CPU.