Let's say we have an app, and there's an in app purchase that unlocks something, let's say for example a pro subscription. You can't buy it from the app itself, because the app is glitched or broken. Is it possible to manually buy this in-app purchase through the App Store?
No. You can only do an in-app purchase through the app (that's the 'in-app' part).
If there's a glitch in the existing app you can either fix it, create a new app, or direct users to your website to make the purchase (there's a bunch of Apple rules about doing that so be sure to check your Apple Developer agreement).