I believe that error can happen if you have not designated any of your replicates as being external standards.
That is, you need to go to the Document Grid ("View > Document Grid"), use the "Views" dropdown to change the View to "Replicates", and, for each of your external standards, change "Sample Type" to "Standard" and fill in a value for the Analyte Concentration.
If that's not what the problem is, then I'm not sure exactly what would be going wrong. You can send us your Skyline document and I can take a look.
In Skyline, you can use the menu item:
File > Share > (complete)
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.
If that .zip file is less than 50MB you can attach it to this support request. Otherwise, you can upload it here: