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.

TV

Blu-Ray

Crunchyroll