I think the problem you're running into is this note in the docs:
I seem to remember running into this before using core image functions, I don't know exactly what the deal is. Using core graphics to crop instead works fine:
// crop using core graphics instead of CIImage
SizeF newSize = new SizeF(500,500);
UIGraphics.BeginImageContextWithOptions(size:newSize, opaque:false, scale:0.0f);
originalImage.Draw (new RectangleF(0,0,originalImage.Size.Width,originalImage.Size.Height));
UIImage croppedImage = UIGraphics.GetImageFromCurrentImageContext();
UIGraphics.EndImageContext();