Hi Ranveer,
Please verify the user profile profile each filter of SharePoint 2016 with SharePoint 2013 - I think some filter mismatch is there - may be in SharePoint 2016 some additional filter has been applied, that is the reason it might led to less users. And the
second thing is - may be the mismatch users what you see are disable or inactive in AD which no more is needed in SharePoint 2016. We also did the migration from SharePoint 2013 to SharePoint 2016, there also we have seen users mismatch but everything was
working fine.
Thanks&Regards,
Habibur Rahaman
C# Corner MVP,Project Lead,MCA,MCSA,MCP,MCTS

Note: If you feel the proposed answer is helpful, please mark as so or if this answered your question,please mark as answer.