Didn't solve the "Instant Warship" mystery, but I noticed something quite annoying: The game ignores walls when you embark/debark ships. (Works for both players and all kind of ships.)
Backstory: Still on my overrun coast, there are some low cliffs I was hoping would be steep enough to prevent landing, but they weren't.
So I built palisades on top.
And observed Carthaginian ships arriving, pointing their nose through the cliff and the wall, and injecting their load of soldiers on top of the cliff, on the other side of the palisade!
Yikes. ...Already walls and fortifications are just a minor annoyance in 0 A.D, and now ships ignore them totally!
I'd rank that "needs to be fixed ASAP", it is beyond ridiculous for a game which prides itself on being historically accurate: Teleporting to shore was invented in 1966 with Star Trek...
Serious now, from what I see, the problem is that collision is determined by a smallish circle in the ships center, while the loading/unloading point is somewhere far on their long noses. Noses which are far outside the bounding box, and thus can pass through anything... I guess the only solution besides changing bounding boxes' shapes, would be to put the loading/unloading point smack in the center of the ship.