Using 0.9.2.10 on WP 3.5.1, I get, every few hours after Minify is enabled, the following alert in wp-admin:
CSS / JS minify cache: File "/home/mysite/public_html/wp-content/themes/style.css" doesn't exist
The front end of the site throws a 500 but nothing gets logged by Apache.
I've disabled Minify completely.