When you have specified an Explicit Retention Time on a molecule, if Skyline detects a peak which overlaps with that retention time, Skyline will choose that peak no matter how low quality it is, or how much better other peaks might work.

If you are planning on training an mProphet model, I would recommend that you clear out the Explicit Retention Time values for all of your molecules.
Then you can use the "Rescore" button at "Edit > Manage Results" to tell Skyline to do peak detection again without those Explicit Retention Time values, and then you will probably have a better set of peaks for the mProphet training to work with.
-- Nick

Hi Nick, thank you so much! Would there be an easy way to do it, once the data is already imported to remove the Explicit Retention Time? Or would I have to improt the transition list again without the Explicit RT and then the data again?

You can use the Document Grid to change the Explicit Retention Time values for all of the molecules in the document.
You would need to create a custom report that contains the "Explicit Retention Time" column.
You can learn about creating custom reports here:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_custom_reports
-- Nick