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.
Comments

No answer, assuming no longer an issue.
Yes its still an issue.
This is still an issue.

What version(s) in particular are you still seeing this issue in? The affects version/s list hasn't been updated since the creation of the ticket, so it's fallen off the radar. 1.7.2? 1.7.9? The latest snapshot (currently 14w18b)?
I have experienced the problem in 1.6.4.

I'll add 1.6.4 to the affected versions list, but unless it can be shown that this still occurs in the latest version, it won't be investigated. 1.6 is no longer under development, and will see no further releases.
Edit: It appears that 1.6.4 can no longer be selected, so it's definitely out of scope, and issues present in that version are no longer considered unless they can be shown to exist in the latest version. At this point, it's probably best to submit a new ticket with your evidence, because the original reporter no longer seems to be monitoring this ticket.
I will try to setup a system to reproduce the bug in 1.7.2 or 1.7.9 and go make a new ticket then. Thank you for the fast replies.

I talked to Covert Jaguar
@ezekielfe I haven't seen it in 1.7, but there hasn't been a MC ver yet where it wasn't. I know they haven't done anything that would fix it
@ezekielfe I'm 100% positive I could recreate it easily enough in 1.7 if I cared to bother.
@unknown, you can have this ticket if you can reproduce it
Is this still a concern in the current Minecraft version? If so, please update the affected versions in order to best aid Mojang ensuring bugs are still valid in the latest releases/pre-releases.
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