users.pull

const userName = "user1", videoName = "video_541d", userId = "user1";
db.createCollection("users");
db.users.insertOne(
    {  
        "userId": "sdsdad-dsdsds",
        "userName": "user1",
        "videos": [
            {
                "name": "video_541d",
                "likes": ["user1", "user1", "user4"],
            },
            {
                "name": "video_3212",
                "likes": ["user1", "user1", "user3"],
            },
        ],
    }
);
db.users.findOneAndUpdate(
    { userName: userName , 'videos.name': videoName, 'videos.likes': userId },
    { 
        $pull: {
          "videos.$[].likes": userId
        } 
    }
);
db.users.find({});