Problem with cell stain intensity

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>> in the tissue sections above, although I am only showing a single (red) channel, but some cells are stained blue, some red and others have BOTH blue and red. I have written a short code to measure intensity of RED in the cells that have BOTH blue and red. The code is as follows (please see attached script for full code)

   Red and blue
   channel_1 = imdilate(red_final,strel('disk',2));
   channel_2 = imdilate(blue_final,strel('disk',2));
   c_r_b = channel_1 & channel_2;

   c_r_b_count = bwconncomp(c_r_b);
   c_r_b_num = c_r_b_count.NumObjects;
   c_r_b_density = c_r_b_num/tissue_area;
   p_r_b = c_r_b_num./red_num;
   p_r_b = p_r_b*100;
   p_b_r = c_r_b_num./blue_num;
   p_b_r = p_b_r*100;

   MeanIntensityValueDoubleStain = c_r_b_count;
     %  T(end). PixelIdxList = MeanIntensityValueDoubleStain; % to display number of pixels  and intensity per pixel for each cell
    C = MeanIntensityValueDoubleStain.PixelIdxList(1,:); %cellarray of all intensities 
    AveragesDoubleStain = cellfun(@mean,C); % getting average intensity of each cell in the array
    AverageOfAllAverageIntensitiesDoubleStain = mean(AveragesDoubleStain); %Average of all average intensities
    T(end).PixelIntensityDoubleStain = AverageOfAllAverageIntensitiesDoubleStain;

The problem I have is the numbers this code is spitting out is higher for figure A (top figure) than for figure B (bottom figure) which can't possibly be correct. Is this because I am running it through imfill? I don't trust the numbers, please correct me where I went wrong.