Grell pointed out that a bolt was found in Todomatsu's room, under his bed. We checked, and it definitely matches the robot that was used to both kill Elizabeth and create a distraction in the fuel reserve.

So—why would it be in his room? Either it suggests something happened in there or it was planted. Of course, the keycard isn't in play here. [ But cough cough, intangibility is, would be the implication. ]