best would be to make a small list of all the css-files on your site and try to exclude them one after the other. this should allow you to optimize most of your css and will allow me to test with the specific CSS which causes problems (if you can provide me with the file).
next to that there's an update of the css-minifier in autoptimize, which fixes a number of regex-issue (which cause internal server errors) which will be in the next version. i'll probably have a first test-version of 1.8.5 available next week.