This answer explains why it happens. To resolve it I call add-migration and name it MERGE and then remove any duplicate migration code that has already happened. This is just to update the model snapshot to reflect the merged model.
Example:
public partial class MERGE : DbMigration
{
public override void Up()
{
// Intentionally left blank.
// This may seem like a hack, but it is necessary when using source control.
// When a migration is created via add-migration, EF creates
// an .edmx file from the current code first classes. It compares this .edmx to the .edmx stored in the last migration before this,
// which I'll call it's parent migration. The edmx snapshots are gzipped and stored in base64 in the resource files (.resx) if you
// want to see them. EF uses the difference between these two snapshots to determine what needs to be migrated.
// When using source control it will happen that two users add entities to the model independently. The generated edmx snapshots will
// only have the changes that they have made. When they merge in source control, they will end up with this:
// Migration | Snapshot Contents
// -------------------------------- | ----------------
// 20150101_Parent Migration | A
// 20150102_Developer 1's Migration | A + Change 1
// 20150103_Developer 2's Migration | A + Change 2
// So calling add-migration will create the current snapshot edmx from the Code First model and compare it to the
// the latest migration's snapshot, which is A + Change 2, and see that Change 1 is missing. That is why it
// creates a duplicate migration. We know that the migrations have already been applied, so the only thing that this
// migration will do is update the current snapshot .edmx so that later migrations work fine.
}
public override void Down()
{
}
}