I can wager another Lele-GX there's some confusion here, and not a bug.
Sometimes checking all the cards of a format or the other is not the easier. And most of the times we miss something like a card in bench doing or preventing something, or we just don't read the text of a card. Or misunderstand it.
No, if I'm using a Standard deck, and if I see cards that look like they are from the HGSS era, then either the selection in duel opponents are too random, or if there is something in the options list I keep missing.
If you're in Standard or Expanded, you can see Judge (Unleashed 78) in play, just because the card has been reprinted (BkP, FLi and LoT) hence you can play the copy you want as it's the same card with a different looking. Same can happen playing Legacy, you can see the Full art Judje LoT 209 in play, and this looks weird sometimes and can be confusing.
You can play a Standard deck in Expanded, and see there HGSS era reprinted cards. And you saw Ghetsis in Legacy. As easy as this.
But you cannot see decks with banned cards for the format or cards from other formats that have not been reprinted. You cannot see a GX in Legacy, or Legend cards in Standard. You wouldn't be allowed to choose the deck. Maybe Unlimited format was selected.
If this would be happening, there would be a ton of threads and Official advertisement about it. However, what you MUST do is send the Game logs to Support. As convinced we are there's no such bug and you are there is, we cannot find a reason and you didn't provide reliable proofs about it. Bugs are not solved here in forums nor Mods will look for the issue, they only answer pre-constructed sentences. So don't fight us, we won't fight you. There's nothing else can be done here. Use the proper communication channels: http://www.pokemon.com/support
WE WANT LEGACY TOURNAMENTS BACK !!! If you also want it, show your support http://forums.pokemontcg.com/topic/55966-feedback-making-it-easier-to-get-the-cards-you-want/
5th day reward packs list http://forums.pokemontcg.com/topic/56679-5th-day-log-in-pack-is-random-got-a-gur-dd/?p=593037
Foro en español, también existe: http://forums.pokemontcg.com/forum/2-español/