My nose is stuffed up and when I clear it the mucus goes into my mouth and I swallow it. Is this bad for you?

No. This is natures way of clearing our nasal passages and respiratory tree. We swallow mucous and secretions all of the time and never know it. The acid in the stomach will kill any bacteria that is swallowed. Certainly one ususally prefers to expectorate this or blow it out by gently blowing the nose. It is impossible not to swallow some of these secretions.
Not really. Swallowing mucous is not "bad". Mucous is present all along the oral cavity, throat, lungs and gastrointestinal tract. May want to see your doctor for the cause of a stuffy nose. Allergies? Sinusitis?