This can happen when you use a transparent grate texture on the floor when there is nothing under it. Just switch the texture in that little piece to the one that's on the rest of the floor. (select the surface of the small piece, then select the big floor area, then hit 's' and click in the texture path field, and hit 'enter') Also, it is good to use playerclip, but if there is nothing under it, then keep it caulk. This advice is based on the first screenshot, as the other one seems to be broken.