Today I used 2 expedition journey cards on a ship, and despite my preset profile for that type of ship, I had to manually distribute the points. I had gotten the first 8 levels using gold, and the points were distributed automatically. But when I used expedition journey they were not.

I could see the argument for why this would be a bug and why it wouldn't.

The reason why is as you stated, ship profiles should update. Could be a simple check that isn't included.

The reason why I could see it not being a bug is because you usually don't just toss expedition journey against just any ship. As such, even if I used ship profiles I would prefer to manually update my attributes for a ship I cast Expedition Journey on.