C# NET Core LINQ To Entities doubling subquery for sorting

It is because EF Core LINQ translator limitations or bad optimizations. I would suggest to rewrite the query using multiple from clauses to achieve the desired result. Here is an example of how you can do this:

var query =
    from entity in _context.MusicalEntities
    from defaultFile in entity.MusicalEntityFiles
        .Where(x => x.IsDefault == true)
        .Take(1)
        .DefaultIfEmpty()
    from lastLesson = entity.MusicalEntitiesToLessons
        .Select(x => x.Lesson)
        .OrderByDescending(x => x.Date)
        .Take(1)
        .DefaultIfEmpty()
    select new DomainMusicalEntity
    {
        Id = entity.Id,
        OwnerId = entity.OwnerId,
        CreationDate = entity.CreationDate,
        Description = entity.Description,
        Title = entity.Title,
        IsPublic = entity.IsPublic,
        IsCompleted = entity.IsCompleted,
        YoutubeLink = entity.YoutubeLink,
        Author = entity.Author,
        UniqueId = entity.UniqueId,
        OriginId = entity.OriginId,
        DefaultFile = defaultFile,
        LastLessonDate = lastLesson.Date,
    };