This might just be a bug in JCloister, or it might be official rules...
Do "lakes" cancel out inns, or lessen their impact? Twice in a game, an road with an inn wasn't doubled, and in both cases, it was moving a ferry that closed the road.
Also, at end game, I'd deliberately scuppered a large inn'd road, which happened to have ferries involved, and it was scored at the end as opposed to zero-pointing.
Linkback: https://www.carcassonnecentral.com/community/index.php?topic=4043.0