This Error has appeared on Aida's route a lot during the beach scene and when I try to do the shopping scene before going to the game the error stays up. I downloaded the 1.1 gigabyte file from this site
Alright, this error is most likely tied to outfits. Have you used Debug Mode and changed character's size? These two scenes you mentioned have outfits that are very specific to sizes they appear and they won't appear properly without a correct size being set. The beach scene is set during size 3, and shopping scene and the entire Kanagawa arc happens on size 4. If you for some reason changed size you have to set it back to correct sizes. Then the scenes should work