Reports of the Aperture 3 upgrade causing library issues have begun to surface. According to a report on The Apple Blog and support forums on the Apple Support Discussions site, people who have attempted to upgrade their existing Aperture 2.x libraries have been experiencing problems when installing the Aperture 3 upgrade. Though no one has found what exactly is causing the issue, it seems to occur when migrating your existing Aperture library during the upgrade process. One possible workaround, if you have not already attempted to upgrade, is to import projects one at a time. This will reduce the amount of stress on system resources and could help you get through the process safely, though somewhat slower.
If you have already upgraded and had the issue occur, you can try rebuilding your Aperture Library (a process similar to iPhoto's). Hold (Command + Option) and click to open Aperture. Choose to repair permissions, repair database, or rebuild the database. Many in the forum report that this has not solved the issue, though starting with a freshly repaired database may not be a bad idea.