Okay, very interesting you have had some similar experience. This is a real mystery since sometimes it seems like they play clean, then another time they can be distorted. I just can't seem to understand what the x factor is. However, I can say that it went away when I sent the audio signal out through a bluetooth device (Bose earbuds and Bose Mini II Soundlink). This makes me think that the problem lies in the hardware of the machine.
So to review...
Distortion occurs unpredictably.
It occurs when listening through MBP speakers or attached headphones or attached Scarlett.
It does not occur when listening through a Bluetooth device paired with the MBP.
Since the loops can be played back without distortion, they are clean presumably.
If you have the time or inclination, maybe you can see if listening via Bluetooth you get the same result (i.e., no distortion)
Rh