Seinaru was planned to have five separate super forms, but this was changed to one, with him gaining other sub forms as a result.
Before facing each historical Witch, Mikoto would have explained their lives, but when it became clear Mikoto wouldn’t be saved until near the end, this was changed to a Purifacator.
There were plans for a Bee and Puppycat chapter, and a chapter for How To Date A Magical Girl!. The former was axed due to being ongoing, and the latter was axed due to the reveal that the entire plot was merely a simulation for a coma patient.