As others suggested (and
Griff pointed out), in
C
you must zero-terminate strings, that is you must append the '\0' at the end of the string.
Try
#include <stdio.h>
#include <string.h>
int main(void)
{
enum { SIZE = 100 };
enum { IN1, IN2, OUT };
char array[3][SIZE];
scanf("%s", array[IN1]);
scanf("%s", array[IN2]);
size_t length = strlen(array[IN1]);
for (size_t n = 0; n<length; ++n)
array[OUT][n] = array[IN1][n] == array[IN2][n] ? '0' : '1';
array[OUT][length] = '\0';
printf("%s\n", array[OUT]);
return 0;
}