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I suggest that you try:

#include <stdio.h>

int main(void)
{
int x = 0, y = 0;
printf("Enter two numbers: ");
scanf("%d %d", &x, &y);
if (x != y)

Sorry, but I cannot duplicate your problem. Input of 5 50 gives the expected result that 50 is bigger.

EDIT:
Just a moment, did you actually enter 5,50 rather than 5 50?