Yeah, but what if bugs are the result of living in simulation? What if "base reality" is so much more such that it is possible for mathematics to be both complete and correct and has solutions for the halting problem? That would actually make it possible to eradicate all bugs in a system.
That's way out there. Once you have that, just ask the question you want answered, why bother with a simulation at all?
Also, the incompatibility between Einsteinian, classical and quantum physics is a pretty big "discrepancy" in the universe, and there may be more exotic physics to be found to explain Dark Matter and Energy.
This applies equally to all reality, though, so it's not a bug, it's a feature. Just because your user cannot understand a feature doesn't mean you didn't intend it to work that way. A bug is a thing that the creators of the software don't understand and didn't intend, and invariably you have a ton of bugs which don't happen uniformly, and thus are really challenging to fix. Reality doesn't have those.