Sounds to me like the exact opposite of the situation the other responders have mentioned. The ext2/3/4 filesystems (and probably some others) by default reserve 5% of the total space for the root user. The "100%" reported by df is 100% of the space available to ordinary users. If you look at the actual block counts, df will report 100% usage whenever the number of used blocks is at or above 95% of the total number of blocks.
I guess it boils down to what you mean by, "but it isn't." If you mean that df is reporting more usage than what you can account for from du, then the responses about deleted files apply. If you mean that there really is still some space available, then that would be the 5% reserved space.
Last edited by rknichols; 05-14-2014 at 08:49 AM.
Reason: Fix "du" vs. "df" mixup. Add 2nd paragraph