Ok.. A few Questions with answers.
Did you buy it from a store? (Game, Gamestop, Toys R Us or any other main store.)
If so then you are lying....If not then your game is not Official and is Tweaked / Hacked although I doubt this because I see nothing on the internet about a Shiny Reshiram in DragonSpiral Tower. Well known hackers always post there hacks on the internet and no Ametuer hacker could do why you witnessed.
Elegant Espeon if you don't know what happened why answer? Anyway I don't think your answer is valid either because Bashing your DS cartridge will not effect the Storyline.
So a word to all users: Bashing your DS Game will not get you a free Shiy Reshiram. It will only break it
The last explanation is that your having been using one of those Hell-Ridden AR cards...
They are pointless your spend 30$ to slowly break your game.
Because you have tweaked with your game you experience glitches.
So if you have a AR its probally to do with that.