Should not be a problem. This happens.
If you want to clarify, use the optional essay to explain to the adcom the discrepancy in the date and that its fairly common in India.
Diplomas and Degree Conferrals
All transcripts from institutions outside the United States must be accompanied by a photocopy of the diploma and/or degree conferral. A degree conferral shows the date, location and institution from which you received an official degree.
I graduated in 1999 but the Degree conferral date shows 2001( I think it happens for any university who are lazy to conduct the convocation on time )..will that be an issue?
Transcripts have the exact date...hoping adcom wont mistake that for an extra 2 years spent at college