While running some minecarts with command blocks on a rail system, they will occasionally merge with other minecarts with command blocks, specifically when they are at the end of a rail that runs into a wall (i.e. a stopping point on a rail network). They merge into one another and you can no longer access one of them unless you push them apart manually.
Is this still a concern in the current Minecraft version 1.7.4 / Launcher version 1.3.8 or later? If so, please update the affected versions in order to best aid Mojang ensuring bugs are still valid in the latest releases/pre-releases.