If you didn't file on time and you're in a refund situation, then nothing to worry. As long as you file within 3 years, you will get you refund and no penalties for filing late. But if you're in a Balance Due situation and you file late without filing an extension, then you will get a late filing penalty, late payment penalty, and interest on the late payment. For now just go ahead and pay your balance due. IRS will bill you later for the penalties.
We live and we learn!! Hopefully you will try to file on time next year!!
All the best!! Thanks for asking this question.