Welcome to the forums @chrisbare!
It is probably because the physics objects are close enough together that Godot wakes all three of them automatically since they are likely to collide with each other given their distance, and from a performance perspective, it is easier to wake all of them at once than wake each individually when there is a collision.
I would try changing the cell_size in the project settings to something smaller than 128 and see if that fixes it. I don't know if that will help or not, but it might, though smaller cell sizes means physics may take longer to execute, leading to less performance.
If you are okay with a script solution, then you could try something like this on the RigidBody2D nodes:
extends RigidBody2D
var force_sleep = true
func _physics_process(_delta):
if force_sleep:
sleeping = force_sleep
Then in the script for moving the RigidBody2D nodes, you just need to do something like:
if "force_sleep" in selected_rigidbody_node:
selected_rigidbody_node.force_sleep = false
selected_rigidbody_node.sleeping = false
And then it should fall like normal, but the other RigidBody2D nodes should hopefully stay asleep and in position.
Also:
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