What does it mean after defragmenting when it tells you some files on the volume could not be defragmented?
Does this mean some files on that drive could not be put in there specific order or arranged correctly?
Just means that some files (such as system or ones in use) could not be defragged. Depends on what software u use, but you could use one with an option to defrag on boot. That way the protected and locked files can be defragged before they're in use.