I am from Nepal. I have a Schengen visa for 3 months and visa was given till June 27, 2015. I have asked Qatar airways to book the ticket to return on June 27, 2015. By doing so I will be back to Nepal in June 28 2015 in which there will be transit in Qatar in June 28. But Qatar airways ticketing staff is telling me that I have to return to Nepal by June 27 which is not possible by flying from there on June 27.
So what can be done?
You do not need to return to your own country before your visa expires, you just need to leave.
However, waiting until the last minute is usually a bad idea. Any delays or rescheduling (bad weather, for instance) will mean you have to deal with immigration in addition to the flight schedule.
Book your return flight for 2-3 days before your visa expires, in your case that's June 25.
If you check in for a flight, and that flight is delayed or cancelled, most countries will give you a short extension. You attempted to leave by the expiry date, the airline prevented you from leaving. It's even easier if you are in the departure area of the airport when the flight is cancelled - you have officially "departed" at that point.
But you will have to go to immigration and explain these things to them. This will take a decent amount of time, and if it is within the last day or two of your visa should be done at the departure airport.
If Quatar air is giving you visa hassles just get a ticket with someone else. Or if they have a toll-free phone number just hassle them into doing it - this requires many, many hours on the phone so make sure you are not paying.