I'm going to talk about the Energy, it's the same for Matter / heat / others.
Currently when you energy reach a threshold you receive a warning. The problem is that when you are recovering energy you get too that warning! Lets say your energy threshold is 100, and your current energy is 120. If you do a shot that cost you 25 energy, your energy drops to 95 and you get a warning. That's ok. However if your energy, after few shots more, is 60 and you rest few turns, once you recover energy and it exceed the threshold you get that warning again!
That's a bit annoying in the middle of a combat, since I think for myself "hey, I think I turned off the energy weapons" or other questions for newbies like me.
What I propose is having two threshholds, the current one and another invisible (i.e. 10% more than the current threshold). So once your energy drops below the visible threshold you get the warning, and you will not get the warning again until your energy exceed the invisible threshold. That would solved the stated problem, and the problem that your energy would be stable in the current threshold and you would get warning every turns.