Whether the symbol next to a transition is red or green depends on whether "Settings > Integrate All" is checked.
If "Integrate All" is checked, the symbol will be green unless the peak area is zero.
If "Integrate All" is unchecked, Skyline checks a few more things such as that the apex of the peak is within one quarter peak width of the apexes of the other transitions.
There is some more information about those colors on page 3 of the Method Refinement tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_method_refine
If you have more questions about your dataset it might be helpful if you 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. The "Share Document" dialog also gives you the option to include your .raw files.
If that .zip file is less than 50MB you can attach it to this support request. Larger files can always be uploaded here:
https://skyline.ms/files.url
-- Nick