When I run this code I get the right answer, why do I fail test #2


import java.io.File;
import java.io.FileNotFoundException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Scanner;

public class EJ1880 {

    /**
     * @param args
     * @throws FileNotFoundException
     */
    public static void main(String[] args) throws FileNotFoundException {
        // TODO Auto-generated method stub
        File Arc = new File("C:\\Documents and Settings\\Admin\\workspace\\ACM\\src\\timus\\datos.txt");
        Scanner in = new Scanner(Arc);
        //Scanner in = new Scanner(System.in);
        ArrayList<Integer> L1 = new ArrayList<Integer>();
        ArrayList<Integer> B1 = new ArrayList<Integer>();

        //Cargar elementos
        int a = in.nextInt();
        for (int aux = 0; aux < a; aux++)
            L1.add(in.nextInt());

        int b = in.nextInt();
        for (int aux = 0; aux < b; aux++)
            L1.add(in.nextInt());

        int c = in.nextInt();
        for (int aux = 0; aux < c; aux++)
            L1.add(in.nextInt());

        //Ordenar elementos
        Collections.sort(L1);

        //Buscar cantidad de elementos repetidos
        for (int i = 0; i < L1.size(); i++) {
            if ((Collections.frequency(L1, L1.get(i)) > 1)) {
                B1.add(i);
            }
        }

        System.out.println(L1.size() - B1.size());

    }

}

You are using frequency for occurrence greater than 1, why not use equal to 3 ?
Also B1 will contain repeated elements, instead try to use HashSet.