Yes, this is due how Steam works, it doesn't keep track of your titles (at all), it tracks your licenses.
And as with so many packs, special editions, etc the Fallout 3 and Fallout 3 GOTY doesn't have the same license, so it will show up as not owned. You actually don't own a Fallout 3 licence, you own a Fallout 3 GOTY licence...

There are scripts here to help with that, that actually checks the present game/dlc for you, but you have to install those as browser add-ons.