Are you asking why the chromatogram graph shows that the areas in the replicate "ontrol_1" are much smaller, but, in the "Peak Areas - Replicate Comparison" graph, the areas appear to be about the same?

In the "Peak Areas - Replicate Comparison" graph, I see that the text on the y-axis says "Median Normalized Peak Areas". That means that Skyline is showing you the actual area divided by the median transition peak area in each of those two replicates. If you want Skyline to show you the actual areas in that graph, you should right-click on that graph and choose "Normalized to > None".

You can read about normalization methods here:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=NormalizationMethods

By the way, I see that the names of your two replicates are "ladeA_1" and "ontrol_1". It looks like those names are both missing the letter "c" at the beginning.
You can fix the names of those replicates using the "Rename" button in the "Edit > Manage Results" dialog.

When you import more than one result file in Skyline at the same time, Skyline checks whether the file names all start with and/or end with the same text. If so, Skyline shows you a dialog which offers to remove the common prefix and/or suffix that all of the names have in common. You can delete characters from the end of the prefix if the prefix is too long and is removing characters that you would like to remain part of the replicate names.
-- Nick