Alternate Character Interpretation: The characters' depictions have generated some issues with the fans; Marisa is more of a Straight Man type, Sakuya is more kindly and gentle than her expected "Perfect and ElegantMaid" persona, and Reimu is a bit of a Jerkass at some points ("Patchouli, get up, we're in the middle of a conversation here!") Since the production is only beginning, however, these remain to be seen.
Must be noted that alternate interpretations abound in Fanon and the abovementioned (with the exception of Marisa) are actually a bit more common than most.
Broken Base: Fans have been divided over whether or not the anime is a perfectly acceptable piece of fanwork, or if it's a complete slap in the face to ZUN's desire to keep the games from being overshadowed.
Internet Backdraft: ZUN's demand for a title change and his accompanying explanation earned lots of flak (at least on Sankaku Complex); things like "He's just butthurt over the fact that the fanworks have become way more relevant than the original games".
In episode 2.5, when Yuyuko was talking to Marisa having seen Alice, she flashed back to the time that Alice ran by her. If you look closely, you can almost see her dull pupils.
Episode 3 takes it further, starting in one of the first few scenes where Alice notices a doll that she doesn't think is hers that she hadn't seen before. Then as she looks around, she sees more of them, and her reaction appears to be horrified shock.
When she's later listening in on a conversation between Marisa and Patchouli, all of a sudden something causes Alice to enter a state where she appears to be growing tired, and one of her dolls falls to the ground as a fog appears.
In one scene, Sakuya hears the doorbell ringing and goes to answer the front door of the mansion, and all of a sudden a disc hits her and knocks her out cold. Patchy quickly turns to see her lying on the ground, flat on her back, unconscious, with one shoe knocked off one of her feet, and jumps down in shock, then checks the outside and finds nobody there. While Sakuya does recover quickly, it still doesn't stray this scene from being creepy in its own right.
Later, Remillia also hears the same doorbell ringing noise that Sakuya heard and starts walking over to the front door, but Patchy grabs her by the arm and tells her not to do that. You could almost tell from Remi's reaction to being stopped by Patchy as a surprised reaction, and Patchy looks absolutely terrified as she is holding on to her. Judging from what happened to Sakuya earlier during what Patchy revealed to Marisa near the beginning, you can tell that Patchy is, in a very terrified way, worried that the same thing could happen to her own dear friend.
Aoi Yuki as Youmu could count: Taking into account she previously voiced Madoka Kaname, one could take as granted Youmu would sound like Madoka. She sounds more like a tomboy instead, compared with her master Yuyuko.