The slip-up entered about Scully all of a sudden having pants on is not right. Watch earlier scenes and look at the pants Mulder is wearing before he finds Scully. They are the same pants Scully is wearing when they all of a sudden appear on her. You might also notice that Mulder has a different pair of pants on, so it's obvious that he was wearing another layer and he took one off to put on Scully. You really think these people would make such a big mistake?