die.rb

class Die

	attr_accessor :selected

	def initialize
		@selected = false
	end

end

die_spec.rb

require 'rspec'

describe Die do

	let(:die) {Die.new}

	describe "#new" do
		it "creates a Die object" do
			expect(die).to be_an_instance_of(Die)
		end

		it "sets selected to false" do
			expect(die.selected).to eq(false)
		end
	end

end

player.rb

require_relative 'die'
require 'debugger'

class Player

	attr_reader :total_score, :dice_set

	def initialize
		@total_score = 0
		@dice_set = []
	end

	def roll_dice
		@dice_set = [Die.new] * 6
	end

	def make_selection(*indices)
		# debugger
		indices.each do |selection|
			index = selection - 1
			die = @dice_set[index]
			die.selected = true
		end
		@dice_set.each {|die| print "#{die.selected} "}
	end

end

player_spec.rb

require 'rspec'
require_relative 'player'

describe Player do
	let(:player) { Player.new }

	describe "#new" do
		it "creates Player object" do
			expect(player).to be_an_instance_of(Player)
		end

		it "sets player's total score" do
			expect(player.total_score).to eq(0)
		end
	end

	describe "#roll_dice" do
		it "generates array of 6 die" do
			expect(player.roll_dice.length).to eq(6)
			expect(player.roll_dice.first).to be_an_instance_of(Die)
		end

		it "sets dice to dice_set" do
			player.roll_dice
			expect(player.dice_set.length).to eq(6)
		end
	end

	describe "#make_selection" do
		it "changes die values to selected with 1 value" do
			player.roll_dice
			player.make_selection(1)
			expect(player.dice_set[0].selected).to eq(true)
		end

		it "changes die values to select with more than 1 value" do
			player.roll_dice
			player.make_selection(1,3)
			expect(player.dice_set[2].selected).to eq(true)
		end

		it "does not change die that are not selected" do
			player.roll_dice
			player.make_selection(1)
			expect(player.dice_set[5].selected).to eq(false)
		end
	end

end

Figured it out (with some help)! In the roll_dice method, I was creating an array of 6 die that were the SAME object.

now it is
6.times {@dice_set << Die.new}
@dice_set