In EF Core 2.0 Identity navigation properties are not included by default, so after upgrading, I added them. So for Many-To-Many relationship between User and Role, and One
I've encountered the same. In my case the problem was caused because I had put the call to base.OnModelCreating(builder) at the bottom of OnModelCreating. Moving base.OnModelCreating(builder) at the very top solved the issue (no duplicate columns and FKs).