Mm.. thinking about it, this arc is actually pretty interesting... From how I see it, Misuzu is probably just overthinking, like Tomo often tells her: she feels guilty because she doesn't want her (only) friend to be taken away by a boy who's more similar to Tomo and who she feels would understand her more, and she thinks Tomo and Jun still aren't lovers because of her half-hearted (but actually pretty effective) advise; but the real reason Tomo and Jun aren't a couple is probably more due to the fact that they are both afraid to change their current relationship. (Sorry for the wall of text, hope it's understandable ^^)