Drupal theming has a trick to exclude CSS file of a base theme in a subtheme. You simply include the filenames of CSS files to exclude it in your info file. Then, if your subtheme doesn't have these files, the files are "overriden" to null state, meaning they are not included on the page.
With AdvAgg these files are still referenced in the page source, probably causing lots of issues (disabled page cache, empty aggregates). But I'm sure this is issue with AdvAgg because when I view the page with ?advagg=0 these files are not included.

Update

I forgot to add this happens not with the base theme CSS files only, but with any overriden CSS files (including core modules').

Files: 
CommentFileSizeAuthor
#4 advagg_skip_missing_theme_files_1844008.patch509 bytescrea

Comments

Basically AdvAgg seems to not completely replicate drupal_get_css() logics.

Title:AdvAgg has problems with overriden CSS files in a subthemeAdvAgg has problems with non-existing CSS files while overriding base theme and module styles
Priority:Normal» Major

This is major, if not critical problem. For me it caused page cache to completely stop working, and caused different strange problems - empty aggregate files, broken CSS links.

I've managed to fix the problem for myself by clearing all non-existant files from the $vars['css'] in my own page preprocess hook.

Title:AdvAgg has problems with non-existing CSS files while overriding base theme and module stylesAdvAgg has problems with missing CSS files while overriding styles in the theme
StatusFileSize
new509 bytes

Status:Active» Needs review

Looks like we also have to clean the advagg_files table from the missing files.

Is this patch works? We are facing problems as when advagg css file is requested we get 404 error sometimes, not always. Is this a related issue as discussed here: http://drupal.org/node/1681712?

Status:Needs review» Fixed

Thanks for the patch it has been committed :)
Open to idea on how to clean up the advagg_files table.

Status:Fixed» Closed (fixed)

Automatically closed -- issue fixed for 2 weeks with no activity.

Issue summary:View changes

update