Welcome! Chickens don’t gather nest material but they do scratch around in the bedding. I’d guess it was in with the pine flakes and they uncovered it.
Actually they can. I use shavings in my nest box (which is right above floor level) but the coop litter is wood chips. Some of my hens will reach out and pick out litter and tuck them into the boxes (and yes I've watched them, so I know it's not accidentally thrown in) - they seem to have a preference for long narrow chips or small branches. Maybe they're bored while sitting in there, who knows? I can tell which boxes are the favorites based on the amount of extras tucked into the nest.