Hey! I've got the same version and I know how to fix your problem. First, to delete the items, highlight one, press A, go to toss, press down, and now you will delete ALL of one item. Just make sure its not one item you need. As for rare candies, find a rare candy, activate the infinte money code and presto! Check your bag. Now for the trainer card, that's normal and it can't be fixed. Sorry! I've got the same problem.
P.S. there's a rare candy behind the weird lady's house in Island 2 at cape brink.