There is a known issue with the original Apogee ONE (the smaller all-black model, not the iOS version or the newer silver version) where input distortion appears when you are at 48k and using Mac OS 10.12 Sierra.
Don't install the Apogee ONE software. The issue doesn't happen if you don't have the Apogee ONE software installed. You can access almost all of the functionality of the ONE in Audio MIDI Setup, System Preferences Sound, or Logic. If you have already installed the Apogee ONE software, you can run the Uninstaller included in the Apogee ONE software package.