She had only been respecting the privacy of his paperwork, his blueprints, she had not meant to make it seem as though she felt slighted in some way. Perhaps he would realize at a later time that she had not seemed offended, merely respectful. Her silence was like his own, not sullen or surly, but rather content with the quiet and with respecting someone else's right to think in peace.
He could have told her not to bow, but for so long as she considered him human and herself mutant, she would continue to do so when taking her leave. She had only managed not to call him sir repeatedly through a sense that he would not appreciate it and the determination that her own habits need not offend one in a station above her. For now, she is slipping back towards the beach, her new sanctuary, leaving him with his own thoughts and the work he feels he should be doing.