While it varies from airline to airline, certainly booking through the airline, or a reputable travel agent helps. As a travel coach, if the prices are the same I always send my clients through the airline, because if something goes wrong with the reservation, or in the booking process the airline is much more likely to help rather than route you through what ever online travel agency you bought your ticket from. Some airlines will help no matter what, but in my experience it is better to either book with the airline, or at least as directly as you can.
Some sources:
http://www.moneytalksnews.com/2012/01/06/avoiding-5-common-issues-with-travel-sites/2/
http://elliott.org/the-navigator/a-problem-with-your-reservation-maybe-your-travel-agency-should-pay/
http://www.forbes.com/sites/larrymagid/2013/04/13/why-i-hate-travel-agencies/
Credit:stackoverflow.com‘