Hey! I'm having the same issue. I'm also too close to harvest to worry but for future reference I'd love to solve this one.
My DWC plant has the rust spots too...like someone took a paintbrush with rust paint and flecked it all over...mostly on the fan leaves. I was at proper PH in RO water and using GH maxigrow ( kept it at about 300ppm ). It really got noticeable when I switched to maxibloom ( started at about 100ppm and slowly lifted it to about 300ppm ). I added a tiny bit of maxigrow to try to keep the Nitrogen more available ( about 30ppm ) and I think it helped...I didn't notice anymore of the spotting but my leaves have yet to start autumn-ing and I'm a little nervous it's because of the extra grow nutes???