The DVD version has various changes (animation improvements, etc). I don't believe Madoka was on Crunchyroll during airing, so is the stream from the DVD edition?
See below for some comparison screenshots from episode 2, at the beginning of the first scene on the school roof (the one where Homura comes and gives a mysterious warning to Madoka and Sayaka).
Judging from the railings surrounding the roof area and the floor tiles, Crunchyroll is using the Blu-Ray/DVD version of Madoka Magica. Not the TV version.