I ended up just uninstalling Wing Commander 1 and 2 and installing each game separately through GoG Galaxy, so problem solved I guess? I just wish it showed up as two games in my library like it's supposed to though. Just like the Ultima series, for whatever reason that's displayed as each game individually instead of the bundle I purchased.
If you're still seeing bundled games on your account page, and you'd rather have the bundles separated into individual titles like on Galaxy, you'll need to do an account refresh. Note that the changes will be permanent, and I don't think that the bundled game download links will be supported much longer anyhow. All of our old, bundled installers, such as WC 1 + 2 are incompatible with Galaxy, you'd need the new, separate installers. https://www.gog.com/account/refresh