The definition of a factory second varies.
For windows and doors usually, product becomes a factory second due to: Being incorrectly entered into the system (wrong size, colour, glass type etc). Builders going bust or not paying their bill (the manufacturer then goes out and reclaims the product from site, so there may be some minor marks from where they were fixed into place). Windows and doors do tend to pick-up minor marks, scratches and dings from handling and storage but there should be no major damage on the product which would prevent it from being operational.