Hi Siva,
Check OMCD, where you can set final delivery completed indicator with GR less than order quantity.
Also check user exit CONPPxx or BADI WORKORDER_GOODSMVT has been active to set final delivery completed indicator upon GR with less than order quantity.
Look in to bellow note for more information.
SAP Note-1857198
SAP Note-2069821
Thanks
Tara