The "red dye" is probably dried loctite because somebody made some tweaker mods on your old crank.
My guess: 1. Pin got loose in the original keyway because of wear or sloppy reinstall of flywheel during a repair. 2. Original owner tried using red loctite to locate the pin, failed. 3. Original owner then drilled a new hole to the best of their ability but it was offset because drilling on a crank arm is hard.