I've encountered this a few times, the no cooldowns takes care of it usually. did see the odd Atlas, it regenerates too fast for me to take down with my Jagermech 2 ac/2's and 2 ac/5's. had to quickly turn off the unlimited armor options to kill it.
I've taken to giving my mech 2k armor all over instead of using the unlimited armor option.
I've also noticed enemies having the no cooldown option set on them. given that I got 2k armor all over I've stopped using that feature as well. currently just have the no cooldown and unlimited ammo active.