this has happened to me a few times as well try targeting it and putting into the console mark for delete or disable as they should get rid of the targeted dragon and do it every time a dragon corpse appears

This has happened to me a few times as well.

Try targeting (i.e., opening the console and then clicking on) the dragon and entering MarkForDelete or disable. Either should get rid of the targeted dragon. Do it every time a dragon corpse appears.