There is a difference between I'm not sure I buy it, and the gut screaming, I don't have the whole story. Be sure you know the difference.
Personally it took me a long time to buy that there was truly NC, and was being followed. because in the early R it was broken repeatedly. But that was different than my gut screaming that his snippy attitude, his quick closing of the computer when I approached, the lock on his phone changing.....
What I did when I had these moments, was to focus on who he was being now. Did he really get it. Did he own his decision, was he doing the work to heal himself, us? That was what mattered. Often that unease is our brains way of giving us a check to be sure we are still safe.
Hang in there look at current behaviors and actions, if they are met with anger, upset, rudness, mean comments, then be alert. If she is kind, understanding, and doing the work, then remind yourself this isn't the person that she was when she committed infidelity. It takes a good while before you start to feel safe.