It would be nice to know exactly what happened here. A couple of other users have reported duplicate built-in prototypes, but I've never seen it happen myself. I think it can only happen during broken Moodle upgrades or installs, particularly if there are issues with the ad hoc task queue processing (e.g. CRON not running).
Did you perform multiple upgrades on the server? Any info you can provide would be helpful.
But to fix the problem proceed as follows.
Firstly you need to find out where the duplicated prototypes are. Logged in as an administrator, click the Home link at the top of the page, then the Question banks link. You should be looking at something like:
There should be a system shared question bank and the CodeRunner prototypes should be in that. The timestamps on the questions might be useful in diagnosing what happened.
In this case, you can safely manually delete one copy of each prototype. They're identified by name, so it doesn't matter which one you delete.
If you're seeing two system shared question banks, each containing CodeRunner prototypes, delete the prototypes from one of them (either one) and if there are no questions remaining in it, delete the bank itself.
Either way, please report which situation occurred and any other info that might help diagnose what happened.