It's bracing itself for the scalpel blade to nick something, because giving humans small weapons, even knives, is usually a bad idea, especially when it involves jabbing them at something. It's giving Levi credit that he's not as inexperienced with them as Amena was (low bar, it knows) but it's bracing since it can't turn down the pain sensors.

Honestly, it figured Levi was going to find a weak point from the outside, not try to pry things up... so it waits, when there's no initial stab of pain, bracing its arm so whatever leveraging or cutting Levi tries next won't be offset by accidental movement.