The most common causes of getting a stinking smell when you floss your teeth are gum disease or periodontal disease.
The gum disease or periodontal disease can cause your mouth to stink or the floss to stink when you floss your teeth.
If you do have gum disease or periodontal disease you should go to the dentist if possible to get checked out because when gum disease or periodontal disease is left untreated it can get worse and lead to tooth loss, infections of your blood and even heart disease in some rare cases.
Your floss or mouth should not stink when you do floss your teeth so you should get checked out by a dentist.
When the dental floss makes contact with the gums then you can get that odor onto the dental floss which is only noticeable when you pull the floss out.
You can do oil pulling to help treat the gum disease as well and gargle with apple cider vinegar which can also kill bacteria in your mouth and help prevent the spread of gum disease.