I had a similar problem with the clone as well as the Banshees. I turned off "unlimited shields" in the trainer and it took care of all that. I left unlimited health on and kept losing shields, but never died. Strangely, though, with my first playthrough with the Citadel DLC, I played a Soldier and didn't have this problem. It was on my playthrough as an Adept and now an Infiltrator that I had the problem. BTW, Infiltrator in this instance was extremely difficult. So I focused on Maya until the clone's medigel ran out then it was just a one shot in the head with the Black Widow (best sniper rifle EVER!! LOL) and then the cutscene.
If your having problem with clone Inf just use 1 of the thermal scopes which is standard on the javelin
I know both options are heavy but I prefer that to having a phantom or nemesis sneak up behind ya
I keep a thermal scope on all my sniper rifles, but I just don't like the the way the Javelin's scope looks when looking through it. The pistol you get with the Citadel DLC, when equipped with the heavy barrel, is such a great weapon that I often only carry the Widow or Black Widow with that pistol. I rarely use a shotgun or SMG, and the new pistol is tough enough that it sometimes renders assault rifles useless unless you really need to lay down a hail of gunfire. Infiltrator has been my favorite class so far because I have always used my squad for close-up stuff while I sit with a sniper rifle and collect head-shots!