birdy

I disabled autoptimize, so you can see them with firebug.

I have three sites:
https://www.fortibase.com (autoptimize enabled and works well)
ozum.wpengine.com (autoptimize disabled you can see all css)
murat.wpengine.com (autoptimize enabled without any other plugin, so fewest CSS)

After cleared cache confirming there is no file then refreshed page:

(I shortened file names for easy read.)
File Permission Group Owner Size
cache 775 33 33
cache/autoptimize 775 33 33
cache/autoptimize/XXX.js 664 33 33 137KB (correct)
cache/autoptimize/AAA.css 664 33 33 71B (broken)
cache/autoptimize/BBB.css 664 33 33 0 (broken)