It was in her miniseries from about a year later. Superman, the Kents, and one of Luthor's ex-wives all tried warning her that Luthor couldn't be trusted. At first she shut them all out. Eventually she wised up, used her shapeshifting powers to do some snooping, and discovered that Luthor was performing protomatter experiments with samples he'd taken from her. Dozens or hundreds of Supergirl duplicates. (Sheesh, talk about alternate costumes!)
After that, she declared all-out war on Luthor. "Hell hath no fury..."