I have a schengen visa valid till 21st Aug'16. My return ticket from Germany are booked for 21st Aug'16. But i shall be reaching India on the 22nd Aug'16 early morning - 3 am. Will this be causing any issue at the Indian airport ?
As an Indian national, you can arrive in India anytime during your life.
It doesn't matter where you came from and what visa you might have needed there or not; the Indian government might not even know, but for sure they don't care.