Would it be unhealthy to have stomach issues 6 days after starting penicillin?

Sometimes: Many antibiotics can cause stomach issues as they kill not only bad bacteria but the good ones that live in your gut as well. If you're having diarrhea, bleeding, or worsening symptoms you should tell your doctor immmediately. Taking probiotics (phillips colon health, align, etc) while on antibiotics can often help with some of the symptoms.