Hi, I have a physical copy of the Witcher 3 that I play through GOG and I just bought the Expansion Pass.
Now GOG is showing me that I have the Game of the Year edition instead and an option to install it (in a different location than the witcher 3) but it doesn't show me an option to actually install the DLC's on top of my existing Witcher 3 game. In fact it still shows me the buy buttons for the dlc's on that page. I don't want to install the game of the year edition but just the dlc's, how do I do that?

Hello. If you are using the Galaxy client and already have Witcher 3 installed through it, try verifying your installation and the game should automatically download and apply the DLCs.

I just did that and it didn't work, also the dlc's are not showing up in my library. Just the goty edition. It says I just have the free dlc and nothing more on the base game. :S on the page of the dlc's it says they are in my library though

Let's see if the client actually recognizes that you have the DLCs. Go to Witcher 3's library entry (not the GOTY) and press the gray "More" button, which can be found right next to the green "Play" button. It should bring up a drop-down menu; select "Backups & goodies". It should show you a screen like the one below:
https://www.gog.com/upload/forum/2019/05/246970ea234afdb3ac2311049d01b644f64dca74.jpg

If you can see the DLCs, that means that you have them, so you should try launching Witcher 3 and the game will tell you that both DLCs have been installed. Otherwise, you can try restarting the Galaxy client and verifying the game's installation again.

Yes, I did restart the client and my pc and verified again, the dlc's are not listed there.

I see.

In that case, you should send a message to support, as something technical seems to have gone wrong and they are the only ones who can help you:

https://support.gog.com/hc/en-us/requests/new?form=account

Fill the fields as necessary and explain to them in as much detail as you can as to what went wrong, so they can help you.

Alright, will do. Thanks for the help.

It's weird you were automatically switched to the GOTY edition, since one of my biggest annoyances with GOG is owning the game and all DLC of many titles like Pillars of Eternity and them NOT doing that.

I wasn't. It was just added to my library, but I still have an active save and didn't want to install another version of the game and start over. Anyway, it is fixed now, I manually downloaded the first expansion from the website and forced it to install and after that the options showed up in Galaxy as well.

With Witcher 3, if you own both expansion, you automatically get the GOTY added to your library. Of course they can do that because CDPR is their sister company.
Although I would really wish if you buy $AnyGame and $AnyEdition Upgrade you would simply own $AnyGame $AnyEdition. Probably some license issue.

Technically, GOTY edition is not different from the base edition except that the DLCs are included by default; your saves would have been fine.
Except Steam does it. It's more likely a limitation with how GOG does things internally here, since everything is a separate product ID, and advanced editions aren't just a collection of the parts like they are on steam, but rather a separate item code altogether.