The timescape was composed of multiple alternate timeline. Large fluctuations in the timescape were detectable by Sphere-Builders, who lived in a trans-dimensional realm.
While Xindi-Reptilian Commander Dolim was in contact with a Sphere-Builder woman, she mentioned the timescape to Dolim. The Sphere-Builder female specifically said that, because minor details of the timescape couldn't be detected by her people because such fine details were obscured, she was unable to extract a launch code that was required to fire the Xindi weapon. (ENT: "Countdown")