Let me suggest that you use the words "town" or "city" instead of just "it" to prevent confusion over what is referenced by "it."
I think the rule is clear on the scoring of cities. What I have found is that new players are confused by what constitutes "linked by rail," and not realizing a break in the rail line at city "A" may result city "B" being disconnected from some towns that are connected to city "A."
Thanks again for making the game.
Good catch Jimmy! Thank you.