Hello @Andrew Fraser
I'm glad that you were able to resolve your issue and thank you for posting your solution so that others experiencing the same thing can easily reference this! Since the Microsoft Q&A community has a policy that "The question author cannot accept their own answer. They can only accept answers by others ", I'll repost your solution in case you'd like to "Accept " the answer.
Issue: Azure B2C not generating a scope for API in JWT
Solution: Resolved by @Andrew Fraser by following the below steps
YouTube video explaining the steps and code required to get the API authentication working. For those struggling with Matt's video, check this one out https://www.youtube.com/watch?v=gxPWRq9BteI this video helps in configuring Azure AD B2C authentication for a web app and web API.
Best regards,
Sakshi Devkante