Can follicles be missed or be hidden behind each other during a scan (fsh have been taken)?

Very unlikely : I assume you're referring to follicles and your ovary. Ultrasound scanning evaluates a three-dimensional structure with a two-dimensional image. The follicles can be identified almost hundred percent of the time if the ovary is visible. It all depends on the skill of the ultrasound technologist or physician and the quality of the equipment being used. The follicles of importance are usually larger and thus much easier to see.