Thanks for the replies. It seems I resolved this issue in another way:
The installed_platform was an array (of filtered children nodes in spaceship node) I cached in physics_process() as it’s frequently used in many places. I observed the errors mostly happened in _timeout() in some Timers. My understanding is that though the Timer is sync with the main _process(), I refreshed the array in physics_process() which can cause async problem. So after I removed the array and always call get_children() directly, the issue disappeared.
But I still have no idea why they look fine in the editor and is_instance_valid() doesn’t help…