Hi
So
The audio coming out of Logic is going in to the Juno, and then out to the speakers, along with any audio that the Juno is making.
You are then using the same audio (out from the Juno) to record back into Logic, and wondering why you end up recording all of it?
You need to read the Juno Manual: Pages 80 & 123 specifically:
From a qucik read, I am not convinced that the setup will work correctly the way you have it now. You may need to consider re-wiring :
Mac out to Amp/Speakers (Logic Preferences:Audio set Output to Built-In)
Juno Out to Mac via USB (Logic Preferences:Audio set Input to Juno)
Create an audio track in Logic to listen to the Juno audio using the Input Monitoring button
CCT