Hi Jess,
I take it that these are extracted from MS1 spectra, then? From an Agilent Q-TOF? Without any ion mobility? Can you fill in a bit more detail and give us a screenshot of the MassHunter view that makes you confident what you are seeing in Skyline is incorrect?
After that, we may need a copy of your document (using File > Share - Complete to create a .sky.zip) and a raw data file (also zipped) that you feel is imported incorrectly for us to take a closer look.
You can upload these files to:
http://skyline.ms/files.url
Hopefully, we can get the issue sorted out quickly once we have the necessary information.
--Brendan