I've been defragmenting with Defraggler and my system crashed (not because of Defraggler).
Does Defraggler defrags 'save', so that he copies the old parts to a new place, makes an new entry in the file system table and then deletes the old part?
Could it be that there are some files destroyed or disappeard now?
If it's using the Microsoft Defrag API which I don't know if it is (you'd have to ask MrG himself about that) a crash or lockup shouldn't cause damage or corruption to files. I don't know if it depends on having NTFS or not.