I can think about two possible solutions, here.
The first one is by using Physics.OverlapSphere. I report the example from the Documentation:
using UnityEngine;
using System.Collections;
public class ExampleClass : MonoBehaviour {
void ExplosionDamage(Vector3 center, float radius) {
Collider[] hitColliders = Physics.OverlapSphere(center, radius);
int i = 0;
while (i < hitColliders.Length) {
hitColliders[i].SendMessage("AddDamage");
i++;
}
}
}
Basically, with this method, you check for the number of colliders that occupy the given area (the area itself is determined by a centre and a radius).
Another, more "basic" solution would be keeping a data structure (like a Map) containing the spawns' informations (like the coordinates of the already instantiated prefabs): this way, you can check directly from the Map if a prefab has been already instantiated here.
Hope this helps!