On the first part of the higher plateau area there's one platform with a wooden bridge leading to another higher platform, with another box.
On the higher cliff path leading to the Flut Flut egg, after the small path past the waterfall, is also a crate.
On the last part of the higher section, past the Eco harvesters, are two taller plateau's. Although one can be reached via a high jump right away, you'll have to raise one of the wooden logs to get onto the other. These logs are located directly under that location, it can be reached via the beach or jumping down the hole in between the two logs. Simply crouch under each log and punch to do an uppercut. After three uppercuts log stump will be raised and you can use them to free each Scout Fly.
On the beach swim across the bay and immediately to your right should be another crate.
At the end of the beach, where the sentinels are you can find this one atop the first sentinel.