Only there's no transistor uniquely responsible for moving stuff up and down. There are transistors responsible for particular bits of output of particular machine code commands, like ADD or MOV. But they are commonly used by almost all the code, so the most probable difference between code triggering the error and a code that's working correctly - would be "how big values we're working on", and if the values are in the "correct" range - that transistor will make a difference. It very well might be that x coordinates are big and y coordinates are low, so it's working for y but not for x. In that particular level of that particular game, assuming the memory was in a particular state before you started that game.
The problem lies in trying to assign too high-level meaning to stuff that works on much lower level of abstraction. It's very similar to alchemy or astrology. Searching for correlation between unrelated events and basing elaborate theories on that.