I am an international student from India and I filed my tax returns through a tax preparer who has used form 1040 for 2008 and 2009. I am on F-1 and my visa was issued in Jan, 2005. I came to know through my friends that I have to use 1040-NR. Is it true? When I confronted my tax preparer, I was told that there is some 180 days rule and I still qualify to use 1040. My wife, who is also an F1 student ( got her F1 in Dec 2006 ) filed her taxes with me ( joint filing ) through the same tax preparer. Are we in trouble for using 1040? Please help us out.
Thank you.

On F1/OPT you are exempt from residency for 5-years. You must file non-resident tax return Form 1040NR or 1040NR-EZ and Form 8843. Your income is not subject to FICA taxes. Your U.S. Tax Return: U.S. Tax Filing Requirements for Non-Residents

You filed resident tax return for 2008, which was a mistake. I really don't know if you will get in trouble or not. Resident must pay FICA taxes. If you are filing resident return as well not paying FICA taxes, evidently this is not correct.

Thanks a lot for your reply.