I'm running Version: 1.17 with 1.03 Entrenchment.

The only way you can lose metal or crystal is by spending it.

Now, it's theoretically possible that your credit income can become negative.  You need to buy population infrastructure upgrades on your planets in order to make their credit income positive, otherwise they drain constantly from your treasury.  This is a common beginner mistake.

If you highlight your resource counter with your cursor, it will show you your total income per second (as well as a per-planet breakdown).

do you have some wierd key binding thing going on where every time you hit one of the mouse buttons (or... anything) it sells metal to the black market?

try resetting your key bindings maybe.

Edit: that would be a totally evil thing to do to an opponent's computer before a game agaist them... ROFL.

In Entrenchment if you have mine layers set to autocast mines they will use resources automatically when they lay mines, I don't remember right now if it is just metal or both metal & crystal of if it is just credits (or all three). In addition if you have set a starbase to be built and the vehicle is still moving towards the location it won't spend the resources until it gets there. None of these should be a constant drain on metal tho. Although the mine layer thing can be a near constant drain if you a lot of them going.