I would guess that it is perhaps just one tile that causes the bug by making the city invisible to the farm.
Perhaps it is worth pointing out to others somewhere obvious that they should check farm scores by hand after their games as it could be the case that this tile joins to a besieged city which is shared between more than one farm with unpredictable results. In this case it didn't change the outcome, but it would be a real shame if somebody discovered that they'd lost a game that they thought they'd won because of it...