Roger I noticed the same issue. You can still get to the top of the poop, but only from the far left (that's the starboard side walking aft). Visually it looks fine, but when you move about you go into the wall and are partially in a Escher-like rear cabin until you walk up that one side. Only half the back deck is solid. Still - what a beautiful model and what a fun ship. V/R AS
I have noticed this with a few ships, i can't name them all but when trying get get between decks which have ladders you have to move the mouse from left to right while trying to go down/up the ladder, but also you have to have your field of vision in the same direction you wish to go ie vision pointing up while going up the ladder and down while trying to go down the ladder, the other thing i noticed which i can't point out all the ships but one is the Constitution, when you go to close to the side walls you can sometimes end up going into them rather than them acting like a abject stoping you from going any further as they should do. I will try to find a list of ships i have experienced problems with and note them all down here for you and what there general problems are, then you can look and see what you think yourself.
Update:
Bellow are some problems i have found with two ships.
Soliel Royal

With masts

After a very unfortunate battle where all the masts was wipped out, i noticed then the rigging waqs still in place, a ship without masts is bad news when its uses a ship with invisable masts is just damn right unfair

:.
Suprise

The ship is missing her picture in the shipyard.

This problem continues after you purchse the ship aswell.

In this picture, not easy to spot but i tried, anyway i can walk from one end of the ship to the other without a single cannon stopping me, in the picture above i'm standing where a cannon is i shouldn't be able to do that, this problem is on both sides of the ship, while the centre of the ship has the hatch for the cargo hold serounded by a rope fence which i can't walk through so some things do work, in my tests it was only the cannons that i could walk right through.
Pink

When sailing in 3D mode the waves are coming upo through the bottom of the ship as you can see.
Hope these help you in some way.