I am not able to rectify the issue in your case since you have not provided the image. But you can see the results on a sample image below without any issue.
im = imread('peppers.png');
P = [100;200]; % coordinates of point within the image size
alpha = 180; % angle for rotation
RotatedIm = imrotate(im,alpha); % rotation of the main image (im)
RotMatrix = [cosd(alpha) -sind(alpha); sind(alpha) cosd(alpha)];
ImCenterA = (size(im,1,2)/2)'; % Center of the main image
ImCenterB = (size(RotatedIm,1,2)/2)'; % Center of the transformed image
RotatedP = RotMatrix*(P-ImCenterA)+ImCenterB;
figure('Name','Before Rotation','NumberTitle','off');
imshow(im);
hold on
plot(P(2),P(1),'r+', 'LineWidth', 20);
plot(ImCenterA(2),ImCenterA(1),'k+', 'LineWidth', 20);
figure('Name','After Rotation','NumberTitle','off');
imshow(RotatedIm);
hold on
plot(RotatedP(2),RotatedP(1),'r+', 'LineWidth', 20);
plot(ImCenterB(2),ImCenterB(1),'k+', 'LineWidth', 20);
(note the change made in line 6,7 for the size function is because I used an RGB image)
The thing here to keep in mind is to reverse the coordinates when drawing/plotting on an image. This is the spatial image coordinates which uses the intrinsic coordinate system. You can find more information regarding it here.
