Fragmentation is a natural side-effect of disk filing systems.
When you delete a file, the file isn't deleted - it is simply marked so that the space it occupied can be used by other files. If those new files are larger than the space available from deleted files, the overspill is put at the end of the data block - thus the file is fragmented. Even screensavers will put paid to any chances of defrag ever completing its task. However, to be fair, Defrag isn't alone in this shortcoming. Some can handle it a little better, however it is best to allow a defragmenter to complete its task before using the machine - unless you're defragging an otherwise idle partition, of coure.