I have analsyed that slowly and steadily people are getting aware that every individuals credit history is recorded by Credit Information of Bureau of India Ltd(CIBIL). Even though you may have cleared all the dues, your CIBIL report may still show them as overdue.
A simple solution is that write an email to your respective card issuer giving them the details and they will report correct information to CIBIL. You may also write a letter to them but it will take more time. Private Financial Institutions have got a tendency to respond to email faster.
In case you financial institution is not co-operating, you may report this to the regional banking ombudsman( https://rbi.org.in/SCRIPTS/bs_viewcontent.aspx?Id=164)