Here you go, here's a scene that shows the problem. In it's current state the population has been cached, and the rogue tree appears at the origin. If you un-tick "use instance cache" and repopulate, the rogue tree goes away. Interestingly, if you re-tick "use instance cache" and render again the unwanted tree stays away, but only until the scene is re-opened or rendered on the render-farm, or the cache is re-saved at which point the tree returns.
I've included a couple of images to illustrate the point.