It happened to me as well during Beta. (and I forgot to post about it... stupid me !)
One easy way to reproduce this is:
* Launch the quest with champion A and lose the fight.
* The goodie hut is now gone, replaced by the remains of the yithril army.
* Attack this stack with another army (in my case, I didn't wait for Champion A to fully recover. I think I had Champion B leading that stack, but honestly I don't remember.)
* Win the second fight.
* Quest is now complete, but Champion A is awarded XP AND the reward and, well, since the city he is recovering in has no access to beach...
* ... You now have a beautiful boat stored in your capital !
i think this is due to the fact that, for some quests, generally when you fail a first encounter and complete it with a second army/champ, it is the champion that started the quest that get the xp/loot/reward.
It's rare and quite hard to notice, though. I thik it happened to me once or twice while playing the scenario.
EDIT:
I've found my saved game ! It's from a late beta (when we first got access to the scenario). I first attempted to kill the Maniac with the champ below (For the record, Gaylin the Gray IIRC) and i only managed to take his army down with a second stack led by somebody named Klunni. The save has been performed one or two turns after the victory and subsequent ship teleporting.
Hope this is useful !
https://www.dropbox.com/s/ppipsv81byv9her/Bug-ship.EleSav