As a brief supplement to Conan and Haibara’s conversation about the rooms of Amanda Hughes and Kouji Haneda, I took a closer look at those sentences in my copy of Volume 89 and tried to provide a translation as faithful and clear as possible.
1: Haibara
それより引っかかるのは荒らされたまま放置されたこの部屋…
[1:それより][2:引っかかるのは][3:荒らされたまま][4:放置された][5:この部屋]…
[1: more than that] [2: what bothers (me)] [3: in a devastated state] [4: left behind] [5: this room] …
More than that, what bothers me is this room that was left behind in a devastated state …
2: Haibara
組織の仕業ならこんな事有り得ない…
[6:組織の仕業なら][7:こんな事][8:有り得ない]…
[6: as for the work of the organization] [7: a thing like this] [8: inconceivable] …
As for the work of the organization, a thing like this is inconceivable …
3: Haibara
何もなかったかのように立ち去るのが彼らのやり方なのに…
[9:何もなかったかのように][10:立ち去るのが][11:彼らのやり方][12:なのに]…
[9: as if nothing had been there] [10: to (stand up and) leave] [11: their way of doing] [12: despite]
Despite leaving as if nothing had been there is their way of doing …
4: Haibara
実際、殺された資産家の部屋はそうだったみたいだし…
[13:実際]、[14:殺された資産家の部屋は][15:そうだったみたいだし]…
[13: in fact], [14: the room of the killed wealthy person] [15: seems to have been like that]
In fact, the room of the killed wealthy person seems to have been like that …
5: Conan
確かに洗面所の蛇口の水も出しっ放しだったって書いてある…
[16:確かに][17:洗面所の蛇口の水][18:も][19:出しっ放しだった][20:って書いてある]…
[16: indeed] [17: the water of the tap of the bathroom] [18: also] [19: was left running] [20: is written]
It is indeed written that the water of the tap of the bathroom was also left running …
Someone who talks about A and then about B will use an anaphoric term in the following sentence for referring to whatever was stated last instead of forcing the hearer to guess which one of the previously mentioned things is meant. In “I had a troublesome dog. Then I had a peaceful turtle. That was much better.”, that only refers to the peaceful turtle and not to the troublesome dog that was mentioned before the peaceful turtle. Correspondingly, I can’t think of any reasonable explanation why Haibara should first (Sentence 1) talk about A (Kouji Haneda’s room “left behind in a devastated state”) and then (Sentences 2–3) contrast A (Kouji Haneda’s room “left behind in a devastated state”) with B (“leaving as if nothing had been is their way of doing”) just to eventually (Sentence 4) utter C (“seems to have been like that”) for referring back not to what was stated immediately before that (“leaving as if nothing had been there is their way of doing” in Sentences 2–3), but to what was stated at the beginning (Kouji Haneda’s room “left behind in a devastated state” in Sentence 1). She is confused by the fact that a room was left in a devastated state although the organization seems to be involved, makes the focus shift by mentioning their usual modus operandi and compares the other room with that (their usual modus operandi). So I agree with Chekhov MacGuffin and Serinox and dare say that every other reading of those words has nothing to do with natural language use.
As for Conan’s reply, I have a minor remark. While it doesn’t change the sense dramatically, I think that the absence of a comma after 確かに (indeed) entails that 確かに (indeed) emphasizes the rest of the sentence instead of directly affirming Sentence 4. To illustrate that, I put indeed after it is; here are the two versions for comparison:
Official Version
確かに洗面所の蛇口の水も出しっ放しだったって書いてある…
It is indeed written that the water of the tap of the bathroom was also left running …
Alternative Version
確かに、洗面所の蛇口の水も出しっ放しだったって書いてある…
Indeed, it is written that the water of the tap of the bathroom was also left running …
I think that, in the latter sentence, Conan would first agree with Haibara explicitly and then mention the rest of his answer to support what she said, whereas, in the first sentence, he would solely emphasize something that supports what she said and might agree only implicitly. Again, the difference wouldn’t be too significant; I just think that the question if Conan agrees with Haibara explicitly or perhaps only implicitly isn’t completely irrelevant either, so I at least wanted to mention it.
I hope this helps to clear things up a bit.