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In the beginning of episode 128, Conan said that he knew Misami, Haibara's sister. However, we have never seen them meet before, how is that possible?

In the next episode, Misami told her sister that she suspects Conan to be Shinichi. I do not think she would think that unless she knew Conan well.

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Akemi Miyano actually was in a previous case, in episode 13, "The Strange Person Hunt Murder Case."

The problem is that the anime didn't do that episode according to the manga, so they had to change some things later to make the show follow the correct storyline.

Here's a summary from Detective Conan World Wiki:

In the manga version of the story Gin and Vodka are the masterminds of the case (rather than Okita), and they end up killing Masami Hirota/Akemi Miyano who informs Conan of the organization's existence and that they dress in black. Her death is the motive of Shiho Miyano's defection which leads to Ai Haibara's appearance later in the series. Furthermore, Shiho makes a silhouetted appearance when Akemi is demanding for herself and her sister to be free of the organization, which is also omitted. To repair the storyline, Episode 128 The Black Organization: One Billion Yen Robbery Case was written with a similar ending to the manga version.

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