You either have not run the extractor or have lots of data exceptions that need to be fixed. This process should help.
1. Run the extractor to ensure that the iProcurement extracted catalog data is updated. See the MOS note below for instructions to run the extractor.
2. Apply the pre-upgrade patch (4914492). It inserts a new entry in the eContent Manager menu called Release 12 Data Migration, which you can use to run the data exceptions report and/or the pre-upgrade.
3. Run the exceptions report prior to the pre-upgrade. The report lists data that cannot be automatically upgraded and must be fixed before the upgrade. The pre-upgrade processes the catalog data to the new data model to reduce upgrade downtime. If there are still exceptions, it also updates the exceptions report. The exceptions report divides exceptions into two categories: those to be fixed using an XML file and reloaded into the catalog, and those to be fixed by correcting system default values.
iProcurement Setup & Usage: Internal Catalog Extract Process [ID 215530.1]