I am an international student. I was suspended for a semester so I decided to get back into the us in fall of 09 on a b1/b2 visa which expired on march 31 2010.

For some reason my university didn't change my status to F1 when I was taking classes in the spring 10 semester which clashed with my b1/b2 visa since I entered in September.

My advisor tells me I have to leave the country and get a new f1 stamp but I read the altercations of overstaying and the whole 3 and 10 year bar for overstaying. Could anyone tell me that if I was taking classes during the overstay period and wasn't aware of my overstay and illegal status, is there a way out without getting into trouble.

I have transcripts stating me taking classes during that period.

From your information, the CIS could determine that you attended school without CIS authorization, a violation of your B visa entry. Even if the school was to file the COS, you are still responsible.

Difficult to get a nunc pro tunc. Consult with an experienced immigration attorney.