That is an easy one.
If it is a conversion kit game, or any Jamma game (dedicated of not), then it may have come with a full harness for it's conversion class, and it simply did not need all the wires.
For example. The NOS Road Fighter kit I have at home came with a full Konami harness, with every wire except for -5 volts (grrrrr).
That means that there are a bunch of unused wires on the harness. Like the wires for the player 2 cocktail control panel. The wires for button #3, etc.