This is a labeling and customer education problem rather than a hoshgocher problem. The OU has no control over labeling and or packaging although they can advice.
The OU is one of the largest and most reliable kosherous organizations, if they had to cancel certification in cases like this they would be out of business and keeping kosher would be very difficult. Many hamisher hashguchas rely on the OU for most of the certification process.
A consumer education is needed to explain that each item that is package separately requires a certification.