If you want some insight into why Skyline has chosen the particular peak that it did, the "Candidate Peaks" window can be very helpful.
You can show that window with the "View > Other Grids > Candidate Peaks" menu item. (In Skyline-daily that menu item has been moved to "View > Live Reports > Candidate Peaks").

The Candidate Peaks window will show you the list of peaks that Skyline detected as well as the list of scores that the peak got which will tell you why Skyline chose the particular peak.
It won't be very helpful in this case where Skyline does not seem to even have detected the peak that you wanted it to detect.

There are only two reasons that I can think of for why there would be a glaringly obvious peak that was not even detected:
1. There is a bigger peak that overlaps with it. The peaks in the candidate peak list never overlap with each other. Sometimes in a screenshot like that the problem is that Skyline thought that peak was much wider than you think it ought to be, maybe because of some transition's chromatogram that you cannot see in that screenshot, and that wider peak that it detected overlaps with the peak next to it, and that's why it did not make it into the list of candidate peaks.
2. Skyline did not actually do any peak detection, and was using peak boundaries from the spectral library. You can tell that Skyline is using peak boundaries from the spectral library because the Candidate Peaks window always has only one entry in it. You can tell Skyline not to use peak boundaries from spectral libraries by using the "Edit List" button at "Settings > Peptide Settings > Libraries" and editing the library entry and unchecking the "Use explicit peak bounds" checkbox. Then you have to tell Skyline to do peak detection again using the "Rescore" button at "Edit > Manage Results".

Other than those two things I cannot think of why your screenshot would look like that.
If you send us your Skyline document we can try to figure out what is going on.
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

Thanks for the detailed response! I've attached the zipped Skyline document from which the screenshot was taken.

Thank you for attaching that Skyline document.

It looks like we have an off-by-one error in the logic for deciding how many candidate peaks to keep.
Skyline notices that there are three candidate peaks which are larger than all of the other detected peaks, but later on ends up rejecting what it had recognized as the largest peak because that peak is not among the three highest-scoring peaks when ranked by other criteria.

I will try to fix this an the next update of Skyline-daily.

-- Nick