Fixed this to use unsigned integers, cleaned up the fread part a bit.

mysort.c

 
 int counter;
 
-int *resize_array(int *a, size_t new_size)
+unsigned int *resize_array(unsigned int *a, size_t new_size)
 {
-    int *save;
+    unsigned int *save;
     save = realloc(a, new_size);
 
     if (save == NULL) {
     return save;
 }
 
-void swap(int *a, int *b){
-    int old_a = *a;
+void swap(unsigned int *a, unsigned int *b){
+    unsigned int old_a = *a;
     *a = *b;
     *b = old_a;
 }
 
-int partition(int *array, int left, int right, int pivot){
-    int pivot_value = array[pivot];
+int partition(unsigned int *array, int left, int right, int pivot){
+    unsigned int pivot_value = array[pivot];
     swap(&array[pivot], &array[right]);
     int storeIndex = left;
     for(int i = left; i < right; i++){
     return storeIndex;
 }
 
-void quicksort(int *array, int left, int right){
+void quicksort(unsigned int *array, int left, int right){
     if (left < right){
         int pivot = right;
 
 
 int main()
 {
+    int temp_size = 50;
     int size = 1;
-    int *numbers = malloc(size * sizeof *numbers);
-    int *temp = malloc(size * sizeof *temp);
-    int error;
+    unsigned int *numbers = malloc(size * sizeof *numbers);
+    unsigned int *temp = malloc(temp_size * sizeof *temp);
+    int ret_val;
 
-    /// Loop through stdin stream grabbing `size` numbers each iteration
-    while ((error = fread(temp, sizeof *numbers, 1, stdin))){
-        // Should not happen if EOF has been reached or we have loaded all data
-        // May happen if we reached EOF at exactly size [didn't find clear documention], in which case next iteration should catch it
-        if (error != 0){
-            numbers[size - 1] = temp[0];
-            size++;
-            numbers = resize_array(numbers, size * sizeof *numbers);
+    /// Loop through stdin stream grabbing `temp_size` numbers each iteration
+    while ((ret_val = fread(temp, sizeof *temp, temp_size, stdin))){
+        // Should not happen if EOF has been reached/we have loaded all data
+        if (ret_val != 0){
+            int new_size = size - 1 + ret_val;
+            numbers = resize_array(numbers, new_size * sizeof *numbers);
+
+            int temp_count = 0;
+            for(int i = size - 1; i < new_size; i++){
+                numbers[i] = temp[temp_count++];
+            }
+            size = new_size;
         }
     }
-    size--;
 
     quicksort(numbers, 0, size - 1);
     for (int i = 0; i < size; i++){