I have a User and an Organization class. They look like this
public class User
{
public int UserId { get; set; }
public string UserName { get; set; }
public string Email { get; set; }
public string FirstName { get; set; }
public string LastName { get; set; }
public virtual ICollection<Organization> Organizations { get; set; }
}
public class Organization : EntityBase
{
public string Name { get; set; }
public string Description { get; set; }
public virtual ICollection<User> Users { get; set; }
}
And both inherit from an EntityBase class to get common fields like Id and created/updated tracking.
public abstract class EntityBase
{
public int Id { get; set; }
public DateTime Created { get; set; }
public virtual User CreatedBy { get; set; }
public DateTime Updated { get; set; }
public virtual User UpdatedBy { get; set; }
}
As denoted by the ICollection properties on both, there should be a many-to-many relation. However when my database is autogenerated I get incorrect foreign keys added to my tables

If I change the CreatedBy and UpdatedBy to be strings instead of User properties I get a join table, which is what I was looking for.

Is this a matter of Entity Framework simply being confused and I need to supply many-to-many configuration in the using fluent mappings, or have I done something wrong?
If you have multiple relationships you need to configure them manually by fluent API or using attributes,
Here is the article from Microsoft.