The menu item conditions on the repair pod terminal (NVDLC04TempleRepairPodTerminal) are such that neither the option to free ED-E nor the warning that security robots are still active will appear, if the Sentry bot and one or both of the turrets were disabled via the Robotics Expert perk. The two turrets are checked only for death, not unconsciousness, thus counting a disabled turret as still active, which is supposed to make the alternative menu item visible - however, if the sentry bot is disabled rather than dead, the conditions apparently evaluate to "false" and thus neither item appears and the player has no sign as to why.
I surmise that the conditions on a menu item are evaluated sequentially, without regard for operator precedence. Thus the condition would be evaluated as (Turret1 not dead OR Turret2 not dead OR Bot1 not dead) AND Bot1 not unconscious, rather than as Turret1 not dead OR Turret2 not dead OR (Bot1 not dead AND Bot1 not unconscious), which means that it is not a complement to the conditions on the alternative menu item, and thus there are conditions under which neither one appears on the terminal.