The MSstats external tool insists that either all of your peptides have q-value, or none of them do.
There is some information about this error here:
That page talks about the two workarounds available to you:
1. You can use "Refine > Reintegrate" so that Skyline will calculate a q-value for everything (you might have to also check the "Override manual integration" checkbox.
2. You can remove the "Detection Q Value" column from the MSstats external tool report in the Document Grid.