According to this Baseballcardpedia.com page, the refractor parallels are Uncirculated (that means they come in a sealed case) and numbered to 25:
http://baseballcardpedia.com/index.php/2004_Topps_Pristine#Going_Going_Gone_Bat_Relics
The page(all the way at the top) also says that each pack had 3 "mini packs". One of those mini packs had an uncirculated card.
Sounds like a Topps goof up to me or Baeballcardpedia.com is missing something (and Beckett for that matter, since Beckett also shows only the uncirculated refractors). I think the Topps goof up is the most likely scenario.