My in-game time counter says that i've played 100 hours, gog counter - 50 hours. Which one should I believe?

First of all, the GOG Galaxy counter increases only if you're playing the game through GOG Galaxy. It won't change if you're launching The Witcher 3 directly. Second, there's a possibility that your internet connection went down when playing the game. In this case the counter won't increase as well.