The two sets of apps are completely independent of each other.
You should not be able to see any of the Azure AD B2C apps in the Application Registration in Azure Active directory.Also, the apps in the Application Registration should not be visible in the B2C .
In your issue , I assume that you should have add two apps in the two places.
What is the differences.
Application in Azure AD B2C :To build an application that accepts consumer sign-up and sign-in, you first need to register the application with an Azure Active Directory B2C tenant.
Application Registration in Azure AD: This creates an Application ID for the application, and enables it to receive tokens. In order to get a client ID and secret from Azure, you have to register the app and provide some basic information about it, including what resources your app wants to access, and what permissions it needs.
Depending on your scenario, you could register an application in both portals, and use the right one depending on the request you need to make.