When rail replacement buses are involved in the start and/or end of a journey, the routeing rules are applied to the points where the rail element starts/ends.
This is not a "mistake" as such however if this produces odd results, a "negative easement" will probably implemented as soon as Rail Delivery Group and/or the relevant train company sees this thread.
If you follow an itinerary to the letter, no-one can deny you travel. They can, in theory,
potentially instruct you to take a more direct route, but they cannot strand you or prevent you travelling to the destination.
A train company could take a photo of the ticket as evidence or they can withdraw the ticket entirely, but if they do so they must issue a replacement ticket that would get you to your destination.
If you would like to learn more about routeing rules or any other fares related matters you are welcome to sign up for a free fares workshop; simply 'vote' in this poll to indicate your preferred venue:
https://www.railforums.co.uk/threads/fares-workshops.208770/