.. yes
Or maybe not intentional, but too hard to fix. I imagine if the water in the boat was intentional, it'd have totally different looking characteristics (a puddle looks totally different from water in a deep ocean, even if it's the same material). It'd be a pain not to get it in the boat.
There's a few ways I can think of to address it, but none of them would be easy:
1.) dynamically tessellate all the water geometry on the outskirts of the boat not to intersect (slow and complicated!)
2.) do some sort of stencil rendering to ensure the interior of the boat doesn't render the water (similar to how stencil shadows work). Also complicated!
3.) Render the hull of the boat only to the depth buffer (no colors rendered), and use multiple passes to make sure the water doesn't clip into the boat.
There's probably quite a few other ways I haven't thought of, but it's definitely not an easy problem.