A guide rail system for guiding containers moved by one or more conveyors, each container having an interior portion defined therein for receiving a product and an opening in fluid communication with the interior portion. The guide rail system includes a cover assembly including one or more cover elements, and one or more structural elements to which the cover element is secured. The structural element locates the cover element in a preselected location relative to the openings of the containers, for at least partially impeding ingress of foreign matter to the interior portions of the containers.