More infomation, like your OS? (Assuming XP) What defragmenter tool are you using?
Have you tried error checking? On my computer right click the drive, properties, tools, check now, tick automatically fix errors but untick bad sectors option. You will probably need to restart your computer (if asked press yes).
It's possible that the defragmenter has determined that the effort needed to defragment those files is greater than the amount of time that would be saved by defragmenting them. (For example a 500mb file in 2 fragments has neglible performance impact).
Apart from this, are there any other problems on your machine? If not, it's probably best not to worry about it.