This game's buffs and debuffs are not very intuitive.
What I think it needs is a new GUI element.
The element would be a top-down picture of your ship, as if from a drawing. If your ship is under some effect, it will show up in this window.
Red flashing weapons = your weapons are being debuffed by something Tactical, like Target Subsystem: Weapons.
Yellow flashing weapons = your weapons are being debuffed by something Engineering, like Aceton Field.
Blue flashing ship = your ship is being debuffed by something Science, like Viral Matrix.
Blue flashing engines = your engines are being debuffed by something Science, like Tractor Beam.
Maybe there are better ways to present it (perhaps some sort of list? Or pictures of every subsystem with red, yellow and blue dots which light up based on what's being impacted?), but basically the idea is to show you graphically why your ship isn't working the way it's supposed to. Some enemy has debuffed you and this window shows you at a glance what's happening.