Once you have manually chosen the correct peak, you might find that the "Edit > Integration > Apply Peak to All" menu item does the right thing.
There is also the menu item "Edit > Integration > Synchronize Integration" which will cause the boundaries in the rest of the replicates to be updated as soon as you make a change to the peak boundaries.

We are also working on a feature "Peak Imputation" which works well when Skyline was easily able to pick the best peak in some but not all of the replicates. You can read about this upcoming feature here:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=PeakImputation

If you are wondering why Skyline chose the peak that it did, you might find some useful information in the "View > Live Reports > Candidate Peaks" window.

If you send us your Skyline document we might be able to give you more advice.

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.

Files which are less than 50MB can be attached to these support requests.
You can always upload larger files here:
https://skyline.ms/files.url
-- Nick