CREATE TABLE [Schema1].[Student](
	[Id] [int] IDENTITY(1,1) NOT NULL,	
	[Email] [nvarchar](max) NOT NULL,	
PRIMARY KEY CLUSTERED 
(
	[Id] ASC
),
) ON [PRIMARY] TEXTIMAGE_ON [PRIMARY]

CREATE TABLE [Shema1].[Course](
	[Id] [int] IDENTITY(1,1) NOT NULL,
	[Title] [nvarchar](max) NOT NULL,
PRIMARY KEY CLUSTERED 
(
	[Id] ASC
)
) ON [PRIMARY] TEXTIMAGE_ON [PRIMARY]

CREATE TABLE [Schema1].[CourseStudent](
	[CourseId] [int] NOT NULL,
	[StudentId] [int] NOT NULL,
	[DateBegin] [datetime2](7) NOT NULL,
	[DateEnd] [datetime2](7) NOT NULL,
PRIMARY KEY CLUSTERED 
(
	[CourseId] ASC,
	[StudentId] ASC,
	[DateBegin] ASC
) ON [PRIMARY]


ALTER TABLE [Schema1].[CourseStudent]  WITH CHECK ADD FOREIGN KEY([StudentId])
REFERENCES [Schema1].[Student] ([Id])
GO

ALTER TABLE [Schema1].[CourseStudent]  WITH CHECK ADD FOREIGN KEY([CourseId])
REFERENCES [Schema1].[Course] ([Id])
GO

    public class StudentConfiguration:EntityTypeConfiguration<Student>
    {
        public StudentConfiguration()
        {
            ToTable("Student", "Schema1");
            HasKey(x => x.Id).Property(x => x.Id).HasColumnName("Id");

            HasMany(x => x.Courses)
                .WithMany( e => e.Students)
            .Map(x =>
            {
                x.MapLeftKey("StudentId");
                x.MapRightKey("CourseId");
                x.ToTable("CourseStudent", "Schema1");   // (1)  тут есть проблема
            });                        

        }
    }

public class CourseConfiguration : EntityTypeConfiguration<Course>
    {
        public CourseConfiguration()
        {
            ToTable("Course", "Schema1");            
            HasKey(x => x.Id);
            HasMany(x => x.Students)
                .WithMany(e => e.Courses);
        }
    }

public class CourseStudentConfiguration : EntityTypeConfiguration<CourseStudent>
    {
        public CourseStudentConfiguration()
        {
            // ToTable("CourseStudent", "Schema1");    // (2) тут проблема есть

            HasKey(x => new { x.StudentId, x.CourseId, x.DateBegin });          
        }
    }

var myContext = new MyContext ()
myContext.Set<Course>().Select(x => x.Id).ToList();

var myContext = new MyContext ()
myContext.Set<CourseStudent>().Select(x => x.StudentId).ToList();

Invalid object name 'dbo.CourseStudent'.

One or more validation errors were detected during model generation:

StudentCourse: Name: The EntitySet 'StudentCourse' with schema 'Schema1' and table 'CourseSudent' was already defined. Each EntitySet must refer to a unique schema and table.