It looks like you have an SRM experiment, but the mass spectrometer only collected data for intact precursors, and there were no fragment ions.
Because of this, the only chromatograms that you are getting for each precursor is the intact precursor chromatogram itself.
Usually, Skyline makes it very difficult to chromatogram peaks at different times for precursors under the same precursor. However, if each precursor has only one SRM chromatogram, then I think Skyline can get confused during the peak finding part of chromatogram extraction, because Skyline is not confident about how the SRM chromatograms should be associated with the precursors.
It looks like you might not have not told your mass spectrometer to collect the data that you actually want. It might be helpful for you to take a look at the Targeted Method Editing tutorial: