I filed a Service Request with Mathworks. They confirmed the issue and provided a workaround which I'd like to share here:
The figure window forwards CTRL+Q to the command window which triggers the closing operation. As a workaround, you can set the preference in MATLAB to "Confirm before exiting MATLAB". Go to preference Under General > Confirmation Dialogs Select "Confirm before exiting MATLAB" Typing "@" first time in a new figure window will trigger the confirmation. Once you hit cancel and proceed to type "@" again MATLAB won't quit. Alternatively, try clicking on the File menu to trigger population of submenus. After that, Ctrl+Q no longer quits MATLAB."
Both workarounds worked in my case.
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