main.rb

class Cell
  @@cellid = -1

  # Renaming the attribute cellid to eg. id makes it work?!
  attr_reader :cellid

  def initialize
    @cellid = (@@cellid += 1)
  end

  def ==(other)
    @cellid == other.cellid
  end
end

def tick(args)
  reset if args.tick_count.zero?
  @cells.delete(@cells.sample)
  args.outputs.labels << [640, 720, "Cells: #{@cells.size}", 5, 1]
end

def reset
  @cells = Array.new(1_000) { Cell.new }
end

mruby.rb

# Simplified version for MRuby, that does not work whatever the attribute name is

class Cell
  attr_accessor :id

  def initialize
    @id = rand(1_000_000)
  end

  def ==(other)
    @id == other.id
  end

  def id
    @id
  end
end

cells = Array.new(1_000) { Cell.new }
1_000.times do |i|
  cells.delete(cells.sample)
end

Simply renaming the @cellid and attr_reader :cellid to eg. id makes the whole thing work.