Apple has identified an "issue" with Time Machine corrupting the Aperture database. Ouch. Since both programs are made by Apple, you'd think they would have figured that one out already.
Issue or symptom
Running Time Machine backup or restore operations while Aperture is running may lead to inconsistencies in the Aperture database.
Mac OS X 10.5 Leopard
If you use Time Machine with Leopard, be sure to set your computer up so that Time Machine only does manual backups. Avoid performing either backups or restores while Aperture is running.
This document will be updated as more information becomes available.