Nova 2 had a bug where if you touch a crate (causing it to turn into a spring, and then turn into air) and then touch the spring (causing it to turn into a pressed spring, then unpressed spring) at the right moment it will schedule popping back up from the spring at a later moment than the block is schedule to disappear and it won't disappear.
I think that's what's going on here too with preventing springs from crates from disappearing sometimes.
Nova 2 had a bug where if you touch a crate (causing it to turn into a spring, and then turn into air) and then touch the spring (causing it to turn into a pressed spring, then unpressed spring) at the right moment it will schedule popping back up from the spring at a later moment than the block is schedule to disappear and it won't disappear.
I think that's what's going on here too with preventing springs from crates from disappearing sometimes.