This sounds like it is caused by a bug in Skyline-daily which we recently discovered where Skyline-daily would completely misunderstand the precursor isolation m/z in wiff2 files.
We released Skyline 23.1 today as well as Skyline-daily 23.1.1.268.
Skyline 23.1 has the bug in it where it misunderstands the precursor isolation m/z in wiff2 files.
Skyline-daily 23.1.1.268 will properly understand which m/z was isolated in the MS2 spectra. However, that Skyline-daily is not able to figure out how wide the isolation window is.
Skyline-daily will work perfectly on your wiff2 data if your MS/MS filtering Acquisition method is "PRM".
If your acquisition method is "DIA", then you might need to go to "Settings > Transition Settings > Full Scan" and explicitly tell Skyline what the isolation width is. That is, the isolation width "Results" or "Results with margin" in the Edit Isolation Scheme dialog will not work with .wiff2 files.
I hope this helps.
It's possible that the problem that you are running into is completely unrelated to this, in which case you could send us your 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.
You should send us that .zip file as well as your .wiff, .wiff2 and .wiff.scan files.
Files which are less than 50MB can be attached to this support request but your files will probably be bigger than that so you can zip everything up and upload it here:
https://skyline.ms/files.url
-- Nick