Raspberry Pi shutdown destroys file system-Collection of common programming errors

I trying to write a small c program witch reads out an GPIO pin to shutdown the pi externally. The triggering of the signal is working well. The program is started by LXDE as autostart application. If the program detects the shutdown signal it’s performing:

sync();
system("halt");

Why does this program damage my ext4 file system after a couple of reboots. There is no fixed number of reboots necessary to damage the system. I don’t see any difference by writing halt to command line. I’m using the newest version of the firmware(last update today) and also the kernel is up to date(last update today).

Does anybody have an good idea about it?