The way I remember it, he was only trying to make one perfect little girl, and even so, she probably wasn't meant to possess superhuman powers, which is what Chemical X brought to the formula.
Otherwise, there was an episode that explained the reason Professor Utonium accidentally added Chemical X was because prior to becoming Mojo Jojo, he was just a mischievous little lab chimp named Jojo who often wrecked stuff in the Professor's lab (much like Dee Dee did to Dexter's), and while the Professor was mixing together the concoction of sugar, spice, and everything nice, Jojo pushed him, causing him to break the container of Chemical X that spilled into the concoction . . . so Mojo Jojo was actually responsible for the Powerpuff Girls' existence.
Otherwise, there was an episode that explained the reason Professor Utonium accidentally added Chemical X was because prior to becoming Mojo Jojo, he was just a mischievous little lab chimp named Jojo who often wrecked stuff in the Professor's lab (much like Dee Dee did to Dexter's), and while the Professor was mixing together the concoction of sugar, spice, and everything nice, Jojo pushed him, causing him to break the container of Chemical X that spilled into the concoction . . . so Mojo Jojo was actually responsible for the Powerpuff Girls' existence.