If you are only seeing fragment transitions on the peak area graph, it might be because you have told Skyline to only display products.

You can right-click on the peak area graph and choose "Transitions > All" to tell Skyline to show both precursors and product ions.
This menu item also controls the display of the chromatogram graph.

If that does not fix the problem then you should send us your Skyline document.
In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.

Files which are less than 50MB can be attached to these support requests. You can always upload larger files here:
https://skyline.ms/files.url
-- Nick