I slowed these two gifs down so you can see the nose wrinkle they each do. In the first gif Mary is asking John if he is going to see Sherlock after work, and wrinkling her nose in support of the idea. In the second gif John is saying ‘yeah, I think so' in response to Mrs. Hudson's comment that Mary is 'lovely’.
I find the symmetry in their expressions interesting because the cute-nose-wrinkle-thing-affirming-someone’s-statement is not something that John does. I can’t think of a single other time he’s done this, and even this time it’s fleeting, coming right at the start of the camera cutting to him. John has adopted a facial quirk of Mary’s - that’s something people do when they are very close, when they are ‘in sync’. It’s a very clever bit of John’s character development by Martin Freeman. Amanda is quite the nose wrinkler in ‘real life’ and I wonder if Martin caught himself picking up on that mannerism early in their relationship.