Birds that spend 99% of their time in a coop/run know very little about "free ranging". Free ranging is a learned/experienced flock behavior that true ranging chickens do virtually all day long as they traverse up to 20 acres or more and travel a quarter mile or farther in doing.
Since your birds only have an hour of free time, they do what's simple, easy and accessible. They dig a hole, they dust bath, they can't/don't go too far, they wear out the same places, over and over again.
You'll have to fence off the areas that you do not want the birds to go, or fence off the chickens into a large run. That's all that can be done. Training that overcomes their natural tendencies isn't very effective. They follow their instincts. Digging, scratching and uprooting is just about a chicken's favorite thing to do.