Your Aperture library may need repairing.
Have you already tried the "Aperture Library First Aid Tools"?
See: Repairing and Rebuilding Your Aperture Library: Aperture 3 User Manual
I'd start with "Repairing Permissions", then "Repair Database", and if necessary "Rebuil Database".
Before rebuilding, I'd recommend to check if the backup of your system is current, otherwise make a backup, before you proceed.