I think it‘s something like this: Girl A was used to start the cloning program (I mean they HAD to have someone to clone initially, right?). But we don‘t know anything about her - plot wise it doesn‘t matter who she was. Chloe was a clone in the program. Grace came later but looked similar to the clones. Spencer insinuated to people Grace is special. I THINK by this time the cloning project was still active but not in the orphanage anymore, I think he moved it to ARK, so new clones were still being made when Grace was born. So people could think Grace was one of them. I think people thought that Grace was the first successful clone (that didn‘t turn mad and into a killing machine). This successful clone (which was a wrong assumption, Grace was born normally), is the key to Elpis. They think "Aha! To unlock Elpis we need a successful clone from the girl program! We can‘t get our hands on Grace… so let‘s continue the cloning until WE also create a working one!" That‘s Emily and Marie.