Do you have the sound on when you play?
Frequently when you talk to NPCs, they will give you something. When they do, there's a sound to indicate that; it interrupts the normal music of the route/ area you're in. That sound, indicating you received an item, must finish playing in order for you to move again. It also happens when you buy drinks from a drink machine (or that dude that sells you Fresh Water in XY).
If you have the sound off, it'll seem like your game has temporarily freezed.