I think it'd be possible that Clem may not remember Molly that well. She wasn't around Clem a lot compared to other characters, and then while not usually a huge thing, Jane has shorter hair so Clementine may have been confused by that. They both looked similar enough, were skilled in killing the walkers, and they both were loner type characters; not really wanting to open up (which is why Jane wouldn't reveal it right away), going so far to want to both leave the group in a similar fashion, by sneaking out with no goodbyes; only difference being Jane came back. Early on, when Clementine looks at Jane, I took it as if she was looking at her wondering if she thought who she was looking at, was Molly.
There was also the conversation Jane and Clementine had, when Jane rejoined, where Jane says something along the lines of "I never had left you before, but..." While not really a strong reason, they are also the only sexually active female characters in the game. I don't think they're the same, but for a good chunk of it, I thought there were many similarities that it was going to be revealed that they were the same. I just think there are a lot of reasons as to why one would wonder if they were the same. In the end it wasn't really something on my mind, but for the majority of it, every time I saw Jane, I kept waiting for her to say she's Molly. Biggest differences is their back stories (which is somewhat similar, as they both had sisters), and difference of voice actresses.
Maybe they were all just supposed to draw parallels to the original crew she was with. Something that could have made me feel this way more so than I originally would have is probably because I was prior to playing Season Two, looking for some wallpaper on Google, and I saw images in which I thought spoiled it (which one did), so it kept me skeptical almost all the way throughout.
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