I found a weird glitch today while practicing a speedrun segment, during a conversation with the cucco lady I was mashing the B button fast and I used my B item during the conversation before she gave me Cojiro...
Maybe "yes or no" questions have a tiny frame of time after them that allows you to use items/move/pause, etc?
http://www.youtube.com/watch?v=PlfMhk_SW3I