Hello Vamsi,
The reason could be that PI has processed the data very slowly and import had happened very lately because it got stuck in the queue. Please check the time in PI for when it is being processed and the time the records go placed in the ready folder.
Or MDIS has processed the data very slowly because of the size or it got another import job to be done at the same time. For this you can check the log files. Log files can be checked in the following directory completely usr\sap\<SAPSID>\<instance_name>\logdirectory. Also you can check the MDIS log under the Auxiliary servers in Console.
Did you check the File aggregation count for that particular inbound port?
Kind Regards,
Thamizharasi N