Yes, you have discovered one of the scoring bugs that keeps many people from playing with the "Basic Rules". In the original boardgame, capturing ships scored you double points - that is in effect here.
However, what is also in effect here is that those double points get erased if the ship is struck while still captured. This in effect allows a player to lose a ship without his opponent scoring any points - and, yes, it is a "must fix" problem with the scoring as it currently stands.