The game does carry the "beta" tag so hopefully these issues get ironed out by the time it releases for iPad because I think a lot more players will start playing the game due to the popularity of the iTune Store. You can submit the problems you encountered to the Pokemon Support Center.
- No Theme Decks for selection at the Trainer Challenge. I bought Dark Hammer and it wasn't shown either.
- I had an occasion where the Day 5 Daily Bonus of a booster pack got skipped and it went to a new Day 1 Daily Bonus. Might be a good idea to screenshot your Day 4 Daily Bonus with your system Date and Time as proof in case it happens. Update: I reported the issue and was awarded a Furious Fists booster pack. The Pokemon Support Team acknowledge that it was an issue and is currently being fixed.