Set variable "arrival" to 0, then set it to 1, 2, 3 once the train arrives at station A, B, C.
Have a Time Check rule starting at the expected time of arrival at station "A", then check every second if the "arrival" variable is equal to 0: if it is, add penalty points to the player score; if it is not (the train has arrived at A and the "arrival" variable has been set to 1) no penalty points will be added.