So, I've tried using it twice in clutch situations, but failed. The first time I didn't exactly throw it at the HE charge, the second time, directly at it. What am I doing wrong? How do I use this effectively?

I dont know if it works on HE Charges... it probably does, I just havent tried it.

I've only thought to use it against turrets. Human players tend to spam Mines and Turrets on that one Hack Objective on the mission where you build the plane as Resistance, so the EMP grenade is amazing there because I can just stroll right through all that and Hack Obj/Turret and spot/destroy mines appropriately.