There was an older version of Lemon's engine which had a lot of bugs like that in it (see: iwbtBoner for a complete set of what bugs there were); once again, I don't actually use water enough in my games to know if they work like that or not, but, in the latest version at least, I don't think there's a problem with the water at all (basing this off of an old dead game of mine that had a water segment, which used the latest version of the engine).