Well you better believe it. Sometimes it's even hard to track down who has the rights in the first place. Companies close, get bought up, get chopped to pieces by liquidators... Sometimes the rights are split between developers, writers and composers. Also GOG needs international distribution licenses. Often one company had publishing right for 'Murica, another for Europe, then there's Asia... Some of them indefinitely, some for limited timespans...

And that's all for games with no third-party licenses (IP, music, cars...) attached.

War Inc. - I wonder if GOG ever tried to bring it here. It was one of the best C&C clones, mixed with R&D and stock market. Great game.