Yeah, that's what they're asking about; In the ending, she says that she ISN'T Krizalid's sister...Zero_D-E350:
And Whip is Krizalids sister, if you use the Ikari team in 99 and win angainst Krizalid, it will explain everything (well, some of it between Whip and Krizalid, anyway ^_^)