Probably the hardware. Every copy of a game might have the same code, but an individual console might have gotten scratched, bumped, a bit humid, slightly burned a connection, food crumbs got in the disk slot and made it read weird for a second, the controller connection is iffy, janky power supply, etc etc etc.
A few years ago a Mario 64 speed runner encountered a glitch that nobody could reproduce. It was eventually determined that the glitch was caused by stray ions from the sun.
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