I think I know exactly what you're talking about. It has occurred in some of my projects.

It sounds like 2 guitars in a single generated track. When you mute all the tracks except that one, it still sounds like there are two instruments playing on it. I have encountered that myself on a few projects. I do not recall the song project or the style or the track. If I recall correctly, even the tone of the 2 guitars was different suggesting that it was a second guitar in the track vs the same guitar playing it all. Is that what you're hearing as well?

In my case, the main guitar sound was a good match for the song, but.... the background guitar sound on that track was not at all what I was looking for in the song and was quite distracting. It changed the entire feel of the song, and not in the direction I wanted.

My solution, and the only one I could come up with, was to choose a different track. I chose a similar guitar instrumental real track, generated it, and replaced the first one, and that seemed to solve the issue.

You can find my music at:
www.herbhartley.com
Add nothing that adds nothing to the music.
You can make excuses or you can make progress but not both.

The magic you are looking for is in the work you are avoiding.