Unfortunately im gonna say that is a game specific issue. The Witcher 3 is DRM free, even when purchased directly from GOG, which means it can be launched at any time without using the GOG client. Which is what i feel is happening here, the game is being launched via its shortcut or .exe, and GOG Galaxy has no idea about it. In fact im guessing you will run into the same issue with any GOG games as well, if its not launched from there client, then its not tracked.