So, there is a moderately advanced civilisation, teleportation, interplanetary missiles, interplanetary system transportation, cloning devices and the like, and the main character walks into a teleportation machine (teleportation works like this: there are multiple bases, you specify which base you want to be teleported to, and the person is converted into energy, the energy at the other teleportation base is used for making the person,) but accidentally clones himself to another telepoertaion base. What could be the explanation for this?
Okay, so this is by no means actually possible, but it makes for a good plot device.
You say that your teleporter works by quantum mechanics which entangle a person into a quantum system, which causes them to trade places with the "energy" on the other transporter.
Except two bases activate at the same time, so he walks out on both bases, one accidentally, and one on purpose. But the energy feedback from splitting him into two locations overloads the original teleporter and causes it to malfunction, (and possibly explode) leaving his clone unable to teleport to his current location until the malfunction is fixed. Boom, two copies of him at different locations.
So, you want to use a teleporter machine for this?
Given that your teleportation machine has certain properties, this is completely possible.
The teleporter must operate by assembling matter at a target location. In your universe, everything required to be a human must be controllable by a teleporter machine. So, the machine normally works by destroying the old self and creating a replica of them at a different teleportation station.
So, it's a replica, rather than just a clone.
When the character enters the machine, something goes wrong and he isn't destroyed like he is supposed to be. The machine still copies him and sends the data to the receiving end, where a duplicate is made. The grim implication is the original normally dies. Maybe the hero figures this out at the last minute and sabotages the process?
Something to consider going this route is your civilization obviously has the tech to make many replicas of people if they want. You'd want to explain why they normally don't allow 2 copies to exist. Perhaps the teleporter companies don't want their customers to realize that teleportation equals instant death.
It's not really a clone... he just thinks it is.
Your plot line can fill in why...
...innocent victim of a teleporter prank call gone wrong...
... the randomly chosen control sample used to calibrate the teleporter was selected from the wrong rack in the freezer and against ALL odds, was his own DNA sample..
... his folks never told him he had had an identical twin, and it wasn't registered in the database because he was a home birth and his parents didn't see the need to report it. The teleporter just followed genetic instructions encoded in the DNA for there to be two bodies created. No one was prepared for this potential until it was too late, and due to ambiguous instruction the teleporter algorithms placed one of the twin bodies at the next closest teleportation location.