If any of your peptides are missing a value for a particular feature (for instance, because the peptide is not present in your spectral library), then Skyline will display the feature in gray italics, and you will not be able to use that feature in your model.

The "Feature Scores" tab in the Edit Peak Scoring dialog shows you what the values are for that feature for the peptides in your document. If the feature is available for some peptides but not others, there will be a bar in the bar graph "unknown". If you move the mouse under that "unknown", a binoculars button appears, and when you press it, the Find Results window will contain a list of all of the peptides missing that feature.

The Library Intensity Dot Product will be missing if the peptide is not present in your spectral library, or if the peptide has fewer than (I believe) 3 product ion transitions.

You can get a more detailed explanation of this in the Advanced Peak Picking Models tutorial starting on page 10:

https://skyline.ms/_webdav/home/software/Skyline/@files/tutorials/PeakPicking_2-5.pdf#page=10

Often you can solve the library intensity dot-product issue by setting a minimum number of transitions that will ensure there will be more than 3 fragment ions. There is now a field for this in Skyline-daily on the Transition Settings - Library tab. Or you can use Edit > Refine > Advanced - Minimum transitions per precursor. (Note: If you have included precursor transitions extracted from MS1, you will need to consider them - for instance, using 6 as the minimum if you have 3 precursor transitions, or 9 if you want your fragment ion minimum to be 6 - as suggested in the original SWATH paper.)

Hope this helps you work out why your document is missing some scores. Thanks for providing screenshots.