Mary looked at Lex with a mix of frustration and pride. It frustrated her at how critically he was questioning her, but at the same time she was proud of how careful he was being. The system really was an entity that was beyond Lex's understanding. It let him confuse beings so much more powerful than him that currently, Lex could not even properly comprehend how weak he was. Using the system, he was affecting events on a galactic scale, if not universal yet. So an adequate amount of prudence was a good thing. It just made things slightly awkward for her.