Moving entities that are crossing chunk boundaries while chunks are loading/unloading have the possibility to either disappear to duplicate. This is pretty easy to duplicate if you put a lot minecarts up running in circles then open/close the game repeatedly. Its also seen when moving into/out of an area. Basically any time chunks load/unload.

I've seen this issue occur many times over the course of the last year and half. And I've had many other people report the same issues. Its been a problem in nearly every large minecart setup I've ever seen, but it also happens to other entities.

If you chunkload an area so the chunks are never load/unloading, it stops happening in that area.