My best guess is that the heart spawns are part of the entity count. Any lag spike and there's a surplus of 'objects' which is the easiest source of errors, especially if the cache doesn't fix itself afterwards. It might confuse the backend into thinking that the new object it's meant to spawn already exists and thus skips it. Lowers efficiency in lust gains, and in my case might be why the Nail didn't spawn until the hard reset of placing a new one.
Not that versed into the inner workings of godot, but sounds legit. Didn’t really think about optimiziation and tested only on my main pc. I did use pooling and other optimization on another game with lots of objects, this was a quicker hackjob so didn’t bother. Gotta keep this in mind for future projects and if I come back to this.