В комментариях указал подробности.
package com.javarush.task.task18.task1808;
import java.io.*;
/*
Разделение файла
*/
public class Solution {
public static void main(String[] args) throws IOException {
BufferedReader br = new BufferedReader(new InputStreamReader(System.in));
String file1 = br.readLine();
String file2 = br.readLine();
String file3 = br.readLine();
try (FileInputStream fis = new FileInputStream(file1);
FileOutputStream fos2 = new FileOutputStream(file2);
FileOutputStream fos3 = new FileOutputStream(file3))
{
byte[] buffer = new byte[fis.available()];
int count = fis.read(buffer); // count = 9
int half = (count + 1) / 2; // half = 5
fos2.write(buffer, 0, half); // fos2.write(buffer, 0, 5);
fos3.write(buffer, half + 1, count); // fos3.write(buffer, 6, 9);
// IndexOutOfBoundsException на 24 строчке, ПОЧЕМУ?
}
}
}