As a result, their computer might be in a strange state. That's not their fault. Your primary goal is not to solve their problem. Your primary goal is to help them become one notch closer to solving their problem on their own. So it's okay if they take notes.
Most user interfaces are terrible.
When people make mistakes it's usually the fault of the interface. You've forgotten how many ways you've learned to adapt to bad interfaces. You've forgotten how many things you once assumed that the interface would be able to do for you. Knowledge lives in communities, not individuals. A computer user who's not part of a community of computer users is going to have a harder time of it than one who is.