I\'m trying to make a relationship between the Users from the table generated by Asp.Net Identity with my own table. The relationship must be many to many, since many Users
Error text is not related to your many-to-many relationship. It tips that other built-in entities are not configured properly. So, It would be nice if you provided full definition of your custom DbContext-class and how it is configured.
UPDATE
As i understood u are working with two different contexts. You must work with the same context, cause of u are extending IdentityContext, creating relationships and adding custom types. So problem then will be resolved itself. Hope, this will help.