Any game-breaking bug is a bad thing, but one that comes up towards the end of your adventure is that much worse. Unfortunately, that's what's been discovered in Paper Mario: The Origami King.
Late in the game, you'll need to get a VIP Card that let's you access a secret passage. This card is passed off to a Toad for verification, which causes the game to autosave. If you continue on your journey from there, you'll be fine. If you talk to Toad again after giving him the pass, he'll completely forget that you've done so, and the game thinks you still need to complete that task. This basically breaks your game and ruins your save file, as there's no way to progress.
Whatever you do, don't talk to the Toad again after you hit this section. Process through the secret passage and then you'll be okay to play as normal. There's no doubt Nintendo will fix this bug, but please be careful until then.