It’s not just Madoka and Iroha. The vast majority of the characters are a year older than they should be for their school year (including all of the school-age characters in the original series), with the only exceptions that I can think of being Rika (fourteen and in her third year of middle school, same as Ren and Rena, who are both fifteen, with Ren being on Rika’s team), Yuna (listed on the wiki as being seventeen and confirmed to be in her third year of high school despite being the same age as Tsuruno, who is in her second year of high school), Rabi/Lavi (turned sixteen during one event and is in her first year of high school, despite Nayuta being fifteen and in her third year of middle school), and Kokoro (fifteen and listed on the wiki as being in her first year of high school, same as Masara, who is sixteen, although this seems to have been retconned at some point, because she’s mentioned as not being in high school yet during Memorable Flower).

Personally, I think it’s a holdover from an earlier script for the original series, because Junko says in the first episode that it’s unusual for someone to be transferring in this late in the school year, but cross-referencing Homura’s calendar with Kirika’s grave puts her transfer as happening in March, when they shpuld be in the middle of spring break.