I cannot reproduce this. I am running 3.2.0.beta2-dev on two separate instances and the remote common.scss files for themes and components seem to be functioning as expected, as is the common css theme editor. Have you tried narrowing it down by disabling other components? Have you made any changes or added any components lately?
If you want to post a link to the theme repository, I can have a look and test it and perhaps see what the issue might be.