Under the menu that lets you save, there is an option called save and calculate shadow map/heights or something simlar. Use that option to remove them.
It is basically the terane and doodad shading generated by that option that has not been updated to match the new terane. Unlike moderngames which use real time rendered shadows, WC3 uses semi pre rendered terane shadows. This is stupid but like I said, simply recalculate them to fix them.