Melody Generator v2 keeps giving me out of scale notes despite settings

[icondark]

I'm struggling to understand something. As the subject says, I'm using Melody Generator v2 and it keeps giving me notes that are out of scale. Even when I enable "Lock to Scale", I am seeing notes that are not in my chosen scale. All of my chords are in the scale. I would have thought keeping notes to a chord and/or scale would be basic functionality but I'm getting notes that are neither. I'm not experienced enough in this software to know if this is a bug or if there's some setting that I'm missing.

EDIT: I added a screenshot. From the coloring, the software knows that certain notes (A3 for example) are out of scale, but I would have thought the Lock To Scale setting (not shown) would take care of that, no?

[Jrmuzik]

It ignores master scale and creates a scale based on the chord. You can cleverly use it to create improvision over certain sections etc. I've attached a screen shot of the manual.