In wow classic era, some alchemy recipes have missing ingredients.

Examples:
Missing Ghost Mushroom and Crystal Vial in both recipes:

I tried looking through the code, but couldn't find out where the data is coming from.

Skillet-Classic gets the recipe reagents through the Blizzard API (running on the client). The Blizzard API gets its data from the server. Unfortunately, there's no Blizzard API function to verify that the client has all the data from the server. Closing and reopening Skillet-Classic usually fixes this issue (and then it will be good for the rest of the session).

Skillet-Classic-1.83-alpha5 contains code that should detect this issue. It does not yet contain code that can recover so you will still have to close and reopen Skillet-Classic.

Reopen this issue (or start a new one) if this is still a problem.