我认为唯一的问题在于你用来洗牌列表的逻辑。

number = r.nextInt(song.size());
boolean done = false;
int counter = 0;
while(!done){
    for(int i = 0; i < songNums.size(); i++){
        if(number == songNums.get(i).intValue()) {number = r.nextInt(song.size()); counter++;}
    }
    if(counter == 0) done = true;
    else done = false;
}

当生成的随机数已经存在于songnums列表中时，您将生成一个新的随机数。这个新的随机数并没有与songnums列表中的所有数字一起检查。下面的更改应该可以解决您的问题。

boolean done = false;
    while(!done){
        number = r.nextInt(song.size());
        if(!songNum.contains(number)) done = true;
    }

或者，您可以在注解中使用sasha的建议来洗牌列表（collections.shuffle（））。

现有算法的实际问题是没有重置 counter 当你发现一首已经播放过的歌曲时。所以一旦你重复一次，你就会陷入一个无限循环- done 永远不会是真的。
（实际上，它不会是无限的——一次 counter 达到 Integer.MAX_VALUE 它会绕到 Integer.MIN_VALUE 最终达到 0 再说一次，如果你把它放得足够长，它最终会播放另一首歌）
关于代码的改进，这里已经有一些有用的建议，我不在这里重复了，但是最基本的修改是移动代码的初始化 counter 至 0 循环内部：

boolean done = false;

while(!done){
    int counter = 0; // reset counter every time

    for(int i = 0; i < songNums.size(); i++){
        if(number == songNums.get(i).intValue()) {number = r.nextInt(song.size()); counter++;}
    }

    if(counter == 0) done = true;
    else done = false;
}

sasha在评论中说：使用collections.shuffle（）。实际上，这看起来像是这样：
在音乐课上，我们有一个方法来获取所有歌曲：

public List<String> getSongs() {return music;}

musicdriver中的循环将沿着以下线路：

List<String> songs = song.getSongs();
do{
    Collections.shuffle(songs);
    for (String songToPly: songs) {
        mp3.playMP3(song.getSong(number));
        System.out.println("Now Playing " + song.getSong(number));
        System.out.println("Enter \"Stop\" to stop playing the song");
        System.out.println("Enter \"n\" to play the next song");
        mp3.stopMP3();
        line = s.nextLine();
        if (!line.equals("n")) break;
    }
}while(line.equals("n"));

在一个变量命名注解中，将music类的示例命名为“song”（单数）有点混乱。也许叫它“音乐”或者至少叫“歌曲”。

我要做的是：

public class MainClass() {

    public static void main(String[] args) {
        PlayerWrapper player = new PlayerWrapper();
    }
}

public class PlayerWrapper() {
    private List<MP3> playlist;
    private Scanner userInputReader;
    private String currentUserInput;

    public PlayerWrapper() {
        userInputReader = new Scanner(System.in());
        System.out.println("Filepath to playlist?");
        String playlistFileName = userInputReader.nextLine();
        playlist = PlayListExtractor.extractPlaylist(playlistFileName);
        start();
    }

    public void start() {
        playlistCopy = new ArrayList<MP3>(playlist);
        shufflePlayList(playlistCopy);
        Iterator<MP3> songIterator = playlistCopy.iterator();
        while (songIterator.hasNext()) {
            MP3 song = songIterator.next();
            songIterator.remove();
            player = new Player(song.toStream());
            player.play();
            displayCurrentSongAndCommands(song);
            currentUserInput = userInputReader.nextLine();
            if ("Stop".equals(currentUserInput )) {
                player.close();
                break;
            } else if ("n".equals(currentUserInput )) {
                player.close();
                continue;
            }
        }

        if("Stop".equals(currentUserInput)) {
            System.out.println("Playlist stopped. Press q to quit or c to continue");
            currentUserInput = userInputReader.nextLine();
            if ("q".equals(currentUserInput)) {
                System.exit(0);
            } else if ("c".equals(currentUserInput)) {
                start();
            }
        }
        start();
    }

    private void shufflePlayList(final List<MP3> playlistToBeShuffled) {
        long seed = System.nanoTime();
        Collections.shuffle(playlistToBeShuffled, new Random(seed));               
    }

    private void displayCurrentSongAndCommands(final MP3 currentSong) {
        System.out.println("Now Playing " + currentSong.toString());
        System.out.println("Enter \"Stop\" to stop playing the song");
        System.out.println("Enter \"n\" to play the next song");
    }
}

public static class PlayListExtractor() {
    private PlayListExtractor();

    public static List<MP3> extractPlayList(final String playListFileName) {
        List<MP3> result = new ArrayList<>();
        try (BufferedReader br = new BufferedReader(new FileReader(file))) {
            String line;
            while ((line = br.readLine()) != null) {
                result.add(new MP3(line));
            }
            return result;
        } catch (IOException e) {
            System.out.println("Problem parsing playlist");
        }
    }
}

public class MP3 {
    private String filename;

    public MP3(final String filename) {
        this.filename = filename;
    }

    public BufferedInputStream toStream() {
        try {
            FileInputStream fis = new FileInputStream(filename);
            return new BufferedInputStream(fis);                  
        }
        catch (Exception e) {
            System.out.println("Problem playing file " + filename);
            System.out.println(e);
        } 
    }

    public String toString() {
        return filename;
    }
}