If you are due a refund, no, there won't be a penalty. If you owe tax, yes, there will be penalties and interest due. The IRS (and State) will send you a separate bill for that.
TurboTax (and most other Do-It-Yourself programs) is not able to prepare the kind of tax return needed for a Nonresident Alien like yourself. You should either consult a tax professional that is EXPERIENCED with Nonresident Aliens, or possibly look for a program that is specifically designed for "Nonresident Aliens".
