Entity Framework Code First Many to Many Setup For Existing Tables

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Remove your Essence2EssenceSet model class. If junction table contains only keys of related entities participating in many-to-many relations it is not needed to map it as entity. Also make sure that your fluent mapping of many-to-many relations specifies schema for table:

mb.Entity<Essence>()
  .HasMany(e => e.EssenceSets)
  .WithMany(set => set.Essences)
  .Map(mc =>
      {
          mc.ToTable("Essence2EssenceSet", "Com");
          mc.MapLeftKey("EssenceID");
          mc.MapRightKey("EssenceSetID");
      });

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