Maybe it's their apologizies or the fact that Jean says he was waiting specifically for her return or the combination of both and everything else including Jean looking so ashamed, that makes her expression soften again. Maru is also helping with that by licking all over her face like Mikasa looks way too serious for her liking and the sudden different mood in the room isn't something, that the puppy likes either...

"It's okay."

It's not like anything bad happened here. Mikasa gives some kisses to the puppy before she lets Maru go and tells him to go play with Snow and Hazel into a room far away from this one. Just in case. She trusts Jean completely but she doesn't trust the werewolf at all with how reckless that side of him could be intentionally or not...

"Well, I'm here now, so how do you want to do that test?"