Yeah that's because of RPGMaker format capabilities, it has some funky autotile limitations where I couldn't fit everything onto the same sheet, so it's not perfect.
Sounds like some tiles might be set up so you can do the old parallax-trick in rpgmaker where the "background image" is the animated base water tile, and then the animations can go over them (the ship tileset had that setup, the beach might allow something similar).
Ultimatey all of the pieces should be there, there but depending on the needs of your project you might need to re-arrange the tiles and animations.
Thanks!