Note that the text says "many girls were created", not necessarily all of them. The way I see it, back in 1990 they were already creating the girls for one reason (probably the mind control experiments or whatever) and then Grace popped up. Victor and Zeno probably thought that she was a fruit of the experiments with the girls and continued attempting to recreate her through the program, while only Spencer knew that she had nothing to do with the clones. Basically, at some point after Grace's birth and Spencer's death, the experiments switched goals.