The previous glass bottle was removed, there is no specific thing to collect the pond one but you need to have visited the madman and the bee hive scene, this is where he gets the idea of collecting the bottle. Until he has the idea of doing it, you can't collect it. If it's still not working, we may have broken your save by removing the empty bottle but seems strange, because I think this would have affected many more players and this is the first report I got on this.