For two cows $A$ and $B$, they will form a crossing point if and only if, when looping over the elements in the circle, the entry and exit points are seen in the order $ABAB$ or $BABA$.

This lets us outline the following $O(N^2)$ algorithm. Loop over the entry and exit points. For a cow of a given breed, we see if we have already seen it or not. If we have not seen it, insert it into a set. Otherwise, remove it from the set, and loop over the remaining elements in the set. Count how many of them were inserted after the element that was just removed.

To optimize this from $O(N^2)$ to $O(N \log N)$, note that we are trying to compute how many numbers were inserted in a specific range of the subarray. We can use a binary indexed tree (BIT) to perform this query in $O(\log N)$ time.

To fully describe the changes to the algorithm, we maintain a BIT that maps indices to $1$ if there was an unmatched insertion at that index and $0$ otherwise. We loop over the points in order. If we haven't seen one before, insert it into the BIT. Otherwise, remove it from the BIT and do a range sum between the current index and the index when the number was originally inserted.

Here is Mark Gordon's code.

#include <iostream>
#include <vector>
#include <algorithm>

using namespace std;

#define MAXN (1 << 17)

int BT[MAXN];

/* Logically executes array[x] += v. */
void bit_add(int x, int v) {
  for(int i = x | MAXN; i < (MAXN << 1); i += i & -i) {
    BT[i ^ MAXN] += v;
  }
}
 
/* Returns the sum of array[i] for 0 <= i < x */
int bit_get(int x) {
  int ret = 0;
  for(int i = x - 1; x != 0; i &= i - 1) {
    ret += BT[i];
    if(!i) break;
  }
  return ret;
}

int main() {
  int N; cin >> N;

  vector<pair<int, int> > A(N, make_pair(-1, -1));
  for (int i = 0; i < 2 * N; i++) {
    int x; cin >> x; x--;
    if (A[x].first == -1) {
      A[x].first = i;
    } else {
      A[x].second = i;
    }
  }
  sort(A.begin(), A.end());

  int result = 0;
  for (int i = 0; i < A.size(); i++) {
    result += bit_get(A[i].second) - bit_get(A[i].first);
    bit_add(A[i].second, 1);
  }
  cout << result << endl;

  return 0;
}