Why are there bound to be bugs? If the universe is the simulation then the bugs are part of the universe and our universe hasn't display any bugs...so why are you worried?
As it has been mentioned before, from the inside any bugs in the simulation will be interpreted as fact. Say somebody discovers free energy due to a flaw somewhere in the simulation's 'sub-subatomic' simulation or something like that. Stuff like that affects how everything interacts and if the entire universe has this flaw in it's makeup then you can't just patch it out without adversely effecting the entire simulation.
Now that free energy puts a considerable extra strain on the simulation, perhaps to the point that if say a nearly an entire galaxy's worth of intelligent life was to use it it would most likely cause the entire simulation to crash. Now intelligent life has rights and there's even talk nowadays that even artificial intelligence will have to be granted those same rights and I bet that in the world outside the simulation will have similar rights. Now if you has a simulated universe with a untold amount of genuine intelligent life inside it you would be bound to do all that was necessary to keep it running, even if that meant the destruction of the species that discovered the bug that could destroy the universe.
This is where your Executioners/Shivans/Great Destroyers come into play... or another species inside the simulation takes it upon themselves to do the job. Heck for all we know we aren't inside a simulation but another civilisation decides that we all are and begins purging all those who the see fit.
With humanity's thirst for knowledge, if we are in a simulator, with bugs, I would be worried about finding that one bug...
(yep, theres a bit of anti-spiral/Vendeeni/4D Being in this post)