I have experienced the same issue as well. The updater doesn't respond when manually unchecking packages to exclude from upgrade. To narrow it down I think it has something to do with the specific package and it's related packages. Until you uncheck all the related packages along with the one you are trying to exclude, the updater doesn't respond properly and have to force quit.
In my case I was trying to exclude Libreoffice from the upgrade, after unchecking it, the updater became unresponsive and cursor kept spinning and I had to kill it from the task manager. On the next try I took a look on all the available packages that are to be upgrade and from their description I noticed how some other packages related to Libreoffice are also available for upgrade. So I tried to unselect those as well. At first I could not able to proceed because the updater kept getting unresponsive when I tried to uncheck the packages. But after a few tries, one time I finally managed to uncheck all the packages related to Libreoffice. And then the updater became responsive once again and the spinning cursor came back to normal and I could proceed with the upgrade afterwards. After that whenever I tried to do so the updater always went unresponsive.
As the workaround I used the following command to mark hold the Libreoffice and it's related packages so that I don't have to go through the same headache again and again:
dpkg -l | grep -i libreoffice | awk '{print $2}' | xargs sudo apt-mark hold
Now everytime I open the updater Libreoffice and it's related packages stays unchecked and disabled and I can continue the upgrade of other pacakges.