That's what shocked me too! and the rat cage has a closed lid but does have a cutout for the top of the water bottle to poke through. The snake pusked the bottle inside and used the hole to get in
Upping the size isn't an option yet, being on mediums is only 2 weeks old and they are just a tad larger than the largest part of his body. I also don't want to power feed him. Maybe I should try cutting back down to smalls and feed him 2?