I got a bug where the Capacitor Discharge is not dealing any damage on enemies.

Ok will look into it later.

I got another bug to report: I changed to Scanning Protocol charges to 3 and the icon indicates it has 3 charges ingame. But it becomes zero after I used the perk.

You changed it to 3 where?

The ability gives all Gremlins base 1 charge. But the mk2 gets an additional change in its ini setting and the Mk3 gets 2 additional charges in its ini setting. If you change the base ability charges to 3 than the mk2 should now have 4 and the Mk3 should now have 5. But if you change ini settings you need to make sure you clean your config ini files or your changes won't take. So the bug you're reporting is a bug you created yourself bud.

Im having a problem in wich none of my tech specialists can hack or haywire protocol eiter (tho Failsafe appearing on the toolbox).
I cant hack turrets, towers and objectives.
Tried look at the .ini but no clue where to look