Usually that error tells you that your Skyline document has an iRT calculator defined, but the document is missing some of the iRT standard peptides.
You can take a look at the peptides that are in your iRT calculator by going to the "Prediction" tab at "Settings > Peptide Settings" and pushing the calculator button and then "Edit Current".
However, considering the fact that you got the error when extracting chromatograms from some but not all of your data files, those iRT standard peptides must be in the document, but, for some reason, during chromatogram extraction, Skyline did not think they were there.
I am not sure exactly how that can happen.
It would be helpful if you could send me your Skyline document and a couple of your raw files. You could send me all of your raw files, or maybe just one .raw file which has an error and one that does not.
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 and spectral libraries.
The Share Document dialog also gives you the option to include .raw files in the .zip file or you could send them to us separately.
Files which are less than 50MB can be attached to these support request.
You can always upload larger files here:
https://skyline.ms/files.url
By the way, if you would like you learn more about using iRT in Skyline, the iRT tutorial has a lot of good information:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_irt
-- Nick