Probably both the filter and the lens (wide open I assume - at 2.8?) introduced heavy vignetting. To avoid this it would have been best to expose to the right (for the highlights) by using a smaller aperture of at least 4, or rather 5.6 / 8 and less ND, no need to shoot so wide open for a wide shot as long as you stay away from extreme apertures beyond 11 or 16.
In post you cold try and see how much you can bring back from the highlights and create a feathered mask to counteract the vignette, although I believe there might be a certain point and area beyond any hope, as a last resource and if reshooting isn't an option you could replace the sky by using a track matte...