Its discomfort levels rise for a perfectly valid and legitimate reason. Murderbot doesn't have all the information, but it can ask for information so it can more accurately complete a threat assessment (its module is throwing errors at it petulantly because it doesn't know how to account for things like controlling ghosts).

"When you say ghost, what do you mean?" Murderbot asks. That's a nice vague question, not nearly so targeted as does that mean you can control Sleepers who have died? That's a giant red 'take away my autonomy' sign if it's ever seen one. It has no intention of giving him that idea if he hasn't figured it out for himself... or better yet isn't relevant.