I cannot tell from your screenshot what might be going on, but if you send us your Skyline document and your raw file (zipped up Bruker .d folder), we might be able to figure it out.
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 can put that .zip file into another .zip file along with your Bruker .d folder, and upload it here:
https://skyline.ms/files.url

In general, if you wonder why the intensity at a particular point along a chromatogram has a particular value, you can click on the point along the chromatogram curve and a graph will appear showing you the spectrum from which the chromatogram point was extracted. Skyline will highlight the regions around m/z values where the intensities were summed to obtain the value which is plotted on the chromatogram graph.
Skyline has some features to look at groups of ion mobility spectra in this way, and you might find some useful information about how to look at the two dimensional ion mobility data around page 13 of the Ion Mobility tutorial:
https://skyline.ms/_webdav/home/software/Skyline/%40files/tutorials/IMSFiltering-20_2.pdf

I am not sure exactly how you expected the chromatogram graph to look in Skyline, but one thing that sometimes happens is that Skyline's interpolation algorithm smooths out peaks.
You can see what the chromatogram looked like before Skyline applied its interpolation algorithm by right-clicking on the chromatogram and choosing "Transform > None".
-- Nick

Hello Nick,

Thank you for the feedback. I tried putting the "Transform" to None but the peak break still appears. I uploaded the Skyline document as well as the raw data by the name "Peak Break files" in the file sharing folder.

Please let me know if further details are required regarding to understand and discuss this issue.

Thank you for the assistance.

BR,
Dhanwin

Thank you for sending those files.

Oops. I misunderstood your original question. I did not realize you were asking about the gap in the curve of the chromatogram line in the chromatogram graph.
That gap is there because "Triggered Chromatogram Acquisition" is checked at "Settings > Transition Settings > Instrument".
You should uncheck that box and then tell Skyline to extract chromatograms again by pushing the "Reimport" button at:
Edit > Manage Results

The Triggered Chromatogram Acquisition checkbox should only be used when you are processing data where the mass spectrometer has been told to start collecting MS2 scans based on something that it sees in the MS1 scans. Thermo has a product called "SureQuant" which is what this feature was designed for. There is more information about SureQuant and the Triggered Chromatogram Acquisition checkbox here:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=TriggeredAcquisition

-- Nick

Hello Nick,

Thank you for the prompt feedback. With the recommended settings, the issue got resolved.

Thanks again for the assistance.

BR,
Dhanwin