This is unlikely to cause problems for personal home directories and such, but it has a disastrous effect when restoring a complete Mac OS X install, if you've done any software updates after your first backup in the set. You'll need to reinstall the OS.
The easy solution (until Dantz issues a fix) is to force Retrospect to backup ALL files, not just changed files.
(The technical reason for the problem is that when Apple updates frameworks in software updates, they update symbolic links named 'Current' to point to the new version. Retrospect backs up the new version, but fails to back up the updated symbolic link. Thus, on restore you end up with the new version, but the old symbolic link -- pointing to a no-longer-present version.)
Wow. I wonder if this is true for older versions too. Maybe I should give up on using Retrospect for a full system backup -- and focus on a data only backup. I can use CarbonCopy Cloner to do a clone periodically, and otherwise only backup the user directory.