You should change the mass analyzer to "Centroided" in the settings on:
Settings > Transition Settings > Full Scan
Also, set the mass accuracy to something small "10ppm".
The peak that you have in the upper half of your "y5" screenshot will collapse down to a single point which will be outside of the m/z channel that Skyline looks at when extracting that particular chromatogram.
After you change settings which affect chromatogram extraction, you need to tell Skyline to reimport the results again, which you can do by going to:
Edit > Manage Results > Reimport
If, instead, you wanted mass accuracy to be one of the characteristics of peaks that Skyline pays attention to when deciding which retention time has the correct peak, you should train an mProphet model. Here's the tutorial for that:
It might be that the y5 transition is not a good one for you to be including, since the thing in the upper pane of that screenshot has a retention time that is so close to the thing that you are looking at. I cannot say for sure without looking at your raw data.
If you want to send us your Skyline document, we might have better advice.
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.
You should send us that .zip file, and that .raw file.
You can upload those files here:
Hope this helps,