Apple suggests disabling Time Machine when Aperture is running :
Time Machine may back up the entire Aperture Library on each run
As a workaround, turn Time Machine off (in Time Machine preferences, in System Preferences). When you want to manually back up, quit Aperture, then choose Back Up Now from Time Machine's menu bar icon (Mac OS X 10.5.2 or later), or by Control-clicking or right-clicking Time Machine in the Dock and choosing Back Up Now.
Translation: We have a nasty bug.
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