I have a question that might help everyone who is having trouble with it. For the scenes where you must wait (example would be the fruit in the farm area) how long must you wait and after what dialogue?
Viewing post in a GROVE timeline comments
It's generally under a minute until the next event triggers, and you can still move around unless you cancel the condition somehow (like by breaking out of the cell in the bandit lair).
In the case of the fruit, there is no way to cancel it after eating it, so you can continue to do whatever and it'll take effect after a delay.