Those bottles, if you're referring to the same ones as I am, were from a video that was shot weeks after she went missing, and about a week or two after she was found. So it's probably safe to say they may have showed up after the police collected evidence. I'm pretty sure they would have gotten them.
But I too wonder about the fingerprinting of the ladder, tanks, and other areas. Rain could have washed prints away (or some of the surfaces may not pick up prints very well). But otherwise it seems that if Elisa was responsible for her own death, then her prints should show up in some obvious places: the cistern, hatch/lid, ladder, etc. But even if they did not find any of her prints and it DID rain between Jan 29 and Feb 19, they wouldn't be able to rule anything out. I'd also be interested in any other prints they may have found on parts of the cistern, although I would think anyone putting her body there would have the sense to put something on their hands... if not gloves, then just a t-shirt, trash bag material, or something.