Many hosts restrict the number of inodes you can use on a VPS or shared account.
If you have shell access, the following commands are useful to determine how many inodes you are using:
ls -R /path/to/directory | /usr/bin/wccd /path/to/directory
for i in $(ls);do echo -n "`pwd`/$i: ";find $i -print|wc -l 2>/dev/null;done