RMXP's ship tiles (inner and outer) are just plain horrendous in many ways, and you've just happened upon the first of them. I think that whoever sprited them was running on a fast deadline and lots of energy mints. You just have to open up a good graphics editing program (or even Paint, although it does strange things if the tileset has transparencies set) and fix the issues yourself. It should be as simple as moving the railing sideways by a few pixels, and I can't see it taking you more than a minute.