If a note is already assigned to a chord (blue keys) then you can’t assign it. If you are using “sections” (orange keys) you can only assign those, again, to notes not already in use.
All this can make “midi learn” a bit tricky. However, you can move the assigned notes up and down, or assign notes not already in use with “Learn.” The whole trick is to not remember that if a note is assigned it can not be “learned.”
Keep working with it. It’s tricky, but the “Sections” can be very helpful and give good results.