I think some careful coordinate system tweaks will get you there. In many Image Processing Toolbox functions, pixels are treated as squares having a width and height of 1. If you want the upper-left corner of your crop region to include the pixel centered at x=1, y=75, then set your upper-left crop corner to be x1=0.5, y1=74.5 so that you are perfectly unambiguous about which pixels are inside the crop region. Then, when you add x1 and y1 back to the coordinates returned by bwboundaries, there is another offset to consider. If the upper-left crop corner is at x=0.5, y=74.5, then the original pixel centered at x=1,y=75 becomes xc=1,yc=1 in the cropped image. If bwboundaries tells you that there is a boundary point there, at xc=1,yc=1, you need to add x1-0.5 and y1-0.5 to shift (1,1) to the expected location of (1,75).
I = imread('coins.png');
x1 = 0.5;
y1 = 74.5;
Iroi = imcrop(I,[x1,y1,150,150]);
GrayRoi = (Iroi);
BWRoi = imbinarize(GrayRoi);
BWRoi = bwareaopen(BWRoi, 100);
BWRoi = imfill(BWRoi,'holes');
[B,L] = bwboundaries(BWRoi,'noholes');
stat = regionprops(L, 'Centroid');
figure('Name','Original+outline');
imshow(I);
hold on;
for k = 1 :numel(stat)
b = B{k};
c = stat(k).Centroid;
plot(b(:,2)+x1-0.5,b(:,1)+y1-0.5,'r' );
end
