In 3rd person limited, when the protagonist is present in a scene, can the narrator describe something in a scene that the protagonist cannot see?
No. In third person limited the narrator can only see what the POV sees. There may be things outside his line of vision that he could hear or smell, which the narrator could describe.
However, in the scenario described in this questions comments, (character clenching his jaw while facing away) could possibly be tweaked to allow description. Your jaw and jaw muscles extend beyond the front of your face. The character could turn his head just enough for his jaw muscles to be seen.
One method to address this is to treat your narrator as a "character", and define the limits and abilities of that character.
From here you can work out ways to define the scope of knowledge of the narrator, what they can comment on, and what they may highlight to the reader.
So you have established that the narrator is not the Focus Character by defining it as a third person, but "How not" the Focus Character are they?
- Is your narrator character exploring the world from within the Focus's own head, looking through their eyes, hearing with Focus's ears, feeling through Focus's skin, etc? [Does the narrator reliably 'read the deepest mind' of the Focus, or can they only see more surface emotions?]
- Is your narrator character "sitting on Focus's shoulder", can they look in another direction and see what the Focus character wouldn't have?
- Are they pulled back even further, following the Focus Character, but able to peek around corners, eavesdrop on conversations [or even thoughts], soar over the scene and give commentary on the Focus Character's situation from a vantage point the FC couldn't possibly be in themselves?
- Is the narrator even Less Limited than that? [At which point you'll be straying away from the 'limited' aspect, but technically a trivial limit is still a limit, and technicality matters... Right?]
You can also use this "Character Designed Narrator" concept to help guide what the narrator knows with regards to time:
- Does the narrator have memory? Did it exist before it began following the Focus Character, and can it make historical references?
- Is your narrator aware of the future? If so, how? How much does it know.
By treating your narrator as a character, with traits, abilities, biases, and whatnot, you can help establish a consistent voice and tone. You could also allow the narrator itself to grow as a character, and change some of its traits over the progression of the story.
Is your narrator something which exist across time with knowledge of the future, a sarcastic jerk who dislikes your Focus Character, and takes pleasure from pointing out how badly things will go?
- You'll end up with a narrator who provides lots of foreshadowing, and highlighting flaws and mistakes.
Is your narrator a kind and hopeful creature trapped in the Focus character's head? - You'll end up with a narrator looking on the bright side of things, and possibly focusing deeper inward to the main character.