Can you post a screenshot? Usually when the shape is too complex to get a good grid fill result, I just go in manually. So if it pokes up a little, you manually scale it all to Z and flatten it or just select the vertex that is doing that and snap it to the level the others are. I don’t think I have ever gotten such an issue with grid fill, so perhaps you changed a setting on the last operation panel and Blender remembers it and is doing that.
