Can you send us your Skyline document and one of your .raw files?
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.
If that .zip file and your .raw file are less than 50MB, you can attach them to this support request. Otherwise, you can upload those files here:
The most common reason that MS2 chromatograms are missing like that is that Skyline did not find any MS2 scans where the isolation window matched the precursor in your Skyline document. When the acquisition method is "Targeted", any particular MS2 scan will only be matched to one precursor in your Skyline document, whichever precursor had the closest matching m/z. Sometimes, there is another precursor in your document whose m/z was closer to what the mass spectrometer said the isolation window was, and so that is the precursor whose chromatogram gets the extracted point. If that other peptide were to have been removed from the document, then your intended peptide would have gotten those points.
We have seen that with SureQuant methods, the isolation window reported in the .raw file is based on what was observed in the triggering MS1 scan, rather than being a theoretical m/z based on the known chemical formula of the targeted peptide. For this reason, there is never a perfect match between the reported isolation window and the precursor m/z. For these sorts of methods, you sometimes have to change the Acquisition Method to "DIA" (and you can use the Isolation Scheme called "Results Only"). Usually, if this sort of thing is happening, what you see is that your MS2 chromatograms have some points in them, but seem to be missing a lot of points from scan which had been intended for that precursor.
There is another feature which Skyline has for SureQuant methods that involves having your method set the "Scan Description" to special values which indicate to Skyline which peptide a particular spectrum was intended for. I can give you more details about this feature if it turns out to be necessary.
For now, it would be easiest if I could take a look at your Skyline and .raw file.