Don't know if this was intended or not, but during the mission "Into the Expanse", if your scanners take damage, no energy is used for the mission, but the mission is advanced.

Is this purposeful as consolation for the extortionate repairs, or is it a glitch that needs fixing?

as far as I know, this also happens on "Weapon Yield Test"

sounds like this is common with missions that damage the players ship.