I see what you mean there, and
I've done it myself.
That is true. What I linked above was caused by my own faulty programming failing to shut down the engine properly and wasting propellant. Instead of just fixing the bug and restarting the test, I decided to roll with it. The result was my best Orbiter experience yet. In fact I'm intending to keep the possibility of the flight computer making mistakes.
But, while I agree with this to an extent, such useable flaws are rare in release-quality addons, and the most common "We've had a problem" scenario is announced by Windows telling you "orbiter.exe has stopped working" - and that isn't very fun, in my opinion.
A great example of what I want to see more of is the random chance of failure that can be set on Thorton's Soyuz rockets, entered as an item in its scenario definition. It's a tiny chance usually, but there's the possibility that your first stage will shut down prematurely, or simply explode, initiating the abort procedures and ejecting the capsule. If that happens during a launch to a space station you've constructed, it introduces a whole new challenge for you, that you did not expect. Did the crew of the aborted mission survive? Do the station inhabitants have a way to return to Earth? How soon can you reschedule the next flight to avoid whatever potential problems that might have just arisen?
Little things like this I think should be included in more addons, because IMO the greatest challenges in the sim are the ones that weren't planned for.