One thing you can do to avoid problems like this, is to always have the "Overprint Preview" on (Main Menu: View + Overprint Preview). This will show you items that for some reason end up as "Overprint Fill" (see "Attributes Window").
What is "Overprint Fill": http://www.kinsmancreative.com/index.php/musings/design-tips/100021-what-is-overprint-fill
Please let me know if this solved your problem. Thank you!