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If you want a story that handles this scenario pretty much exactly, you might want to check out “Unsong” [0] by the excellent Scott Alexander.

That world is basically a biblically-inspired computer simulation which gets corrupted when Apollo 8 crashes into the celestial sphere. Also boiling a goat in its mother’s milk causes a segfault for some reason the developer can’t quite explain.

[0] http://unsongbook.com/chapter-1-dark-satanic-mills/