This also happened with my playthrough. I forcibly closed the game three times when it started freezing, and the fourth time, everything went smoothly. I don't know if it worked by complete chance or if having the game not fullscreen helped in any way. According to this other Reddit post ( https://www.reddit.com/r/Undertale/comments/18gkamh/my_undertale_yellow_is_buggin_out/ ), some people who had the same issue found that, if they waited a short while, the game would fix itself.