The file system is what keeps track of where your data is and how to retrieve it when you need it. Basically it consists of a directory of file and folder names, and a pointer to a location on the disk where that file's data resides. There is a separate listing of which sectors on the disk are free, in-use, or faulty. Normally DOS and Windows handle these reliably. There are times, however, when something gets forgotten.
Improper shutdown is probably the most common cause of file system problems.
Two common errors that might occur are lost clusters and cross-linked files. A lost cluster is one which is marked as being in-use, but there is no directory entry that points to it. It essentially takes up space, but provides not benefit. Usually these can just be deleted. One sector is pointed to by multiple directory entries.