It's because there are two different partitions on the card, one is PI_ROOT which is mounted at /, and the other is PI_BOOT and is mounted at /boot.
It's been widely discussed:
It seems to be a problem with Software Updater, which doesn't take into consideration that it's not a desktop image, /boot on a Raspberry Pi doesn't need the amount of space then that of the desktop version.
A workaround is to upgrade through Synaptic, or through the terminal:
sudo apt dist-upgrade