I don't know which was the intention of that player putting the two tokens below the city, but that's not illegal and you only have to select the city to see all the counters inside that selection in cyberboard's display area, so I don't see anything versus the rules. PBEM it's different than a real game. Anyway I have to say that if the intention of that player was to hide that two tokens to other players this it's something near to cheating, and personally I don't like that type of actitude playing a game.
IMHO in this case the decision it's up to you, but a nice solution would be to pass it this time and let clear to all the players that for future turns tokens in city areas MUST be over the cities.
Regards.
Jon G.
www.civiboard.com/hellas/index.html