Hi Nagar,
Try to run once again ABAP program through t-code SE38/SA38 RMBWV3XX ( xx is application like 02, 11, 12,13) and then run Infopackage and check it take zero records or not.
After this still you are facing the problem check below t-code and tables
SMQ1
SM13/LBWE
RSA7
It might be the case data is not properly moved to BW.
Check setup table - MC*SETUP in SE16. and delete setup table data through t-code LBWG.
Hope this helps,
Chandresh