Swapping "A" and "Y" while using a gamepad causes the first line of dialogue to be skipped after a prompt.

[EvilFriedBacon]

By default, A is Jump and Y is the interact key. However, it seems A is also a skip button by default and there isn't a way to change that. So, for example, when given a Yes or No response or talking to a shopkeeper from a menu, the next line right after it is skipped as the game registers your skipping the line of dialogue because you pressed "A" which is a skip button.