The horizontal lines in the chromatograms happen when there are no MS2 spectra which match your precursor over a period of time in the chromatography. This is expected to happen with DDA experiments, and for this reason, chromatograms extracted from DDA experiments are not useful.
It looks like you have a scheduled PRM experiment, and the machine did not start collecting MS2 spectra for that precursor until a little after 25 minutes. I think both of the chromatograms in your screenshot have those long horizontal lines, but in the lower panel the first MS2 spectrum had lower intensities, so when Skyline extended the lines horizontally, the lines ended up being closer to the X-axis so you can't really see them.
I would have to see your files to know exactly what is going on. Skyline tries to truncate the chromatograms in PRM experiments so that the chromatogram does not extend beyond the range where there were matching MS2 scans. I am not sure why that did not happen here. It might have something to do with other precursors in the same peptide.
If you would like, you can send us your files.
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 can upload that .zip file here:
It would also be helpful to see a few of your .raw files.
I am not sure I understand your question about mProphet. I believe there is no way to tell Skyline to skip over a particular replicate for a particular peptide. Skyline looks at all of the possible peaks for all of your peptides and tries to come up with the best weighting of features in order to get the best separation between your targets and decoys.
Hope this helps,