As an ATC I know these happen but just don't understand why? The movement and placement of strips in a tower environment should be a simple, systematic yet logical way of ensuring these type of incidents don't happen. ie when you clear an aircraft / vehicle / maintenance crew to enter a runway you physically place a strip in the clear to land slot. Then if you clear an aircraft to land you physically have to wonder why you can't fit two strips in the one slot and hopefully bells ring. I might be old fashioned but these old fashioned systems just seem to work.
Regardless of how busy or how quiet you are if you stick to the system so that it becomes automatic ALL THE TIME. then hopefully that system is what keeps it all on the rails.