You have not referred to the period as to whether it is FY or AY. However from the body of the query it appears to be financial year. Based on this assumption, in my opinion you should advise the assessee to revise the return for AY 2011-12 (FY 2010-11). As stated by you the error was due to software glitches so you have strong case to avoid levy of penalty for concealment after revising the return.
If return is not revised then the assessee will be open to proceedings U/s 148 rws 147 and resultant penal consequences.
If return is not revised then the assessee will be open to proceedings U/s 148 rws 147 and resultant penal consequences.