Sorry if i'm just blind, but i can't find where it labels how many charges you have left in your Ammo Case when you use it, also, i didnt see it in the list of things i can choose when doing system trauma (I had only used 1 out of 6 charges, assuming its actually keeping track)

It’s a bit tucked out of the way, but the charges are shown in Walking Armory tooltip within your “active effects” list:

It would probably be a good idea to surface that better somehow while you’re picking an option.

For the system trauma issue: good catch! I didn’t realize it should be a valid target. Logged :)