It might be the Fire TV not recognizing your voice. Try putting a message through a text to speech and see if the Alexa would understand that. Otherwise, I have no idea.
It might be that it’s a software issue, in which you’d need to reinstall the 3DS’ OS. If not, maybe the home button short circuited. I’m not an expert on the topic, though, so more people might be able to give better responses.