Agreed, lack of monitoring the prisoners and be totally oblivious to the fact that Peter was being manipulated by Adam was way boneheaded for an organization like The Company.
Unless the whole thing was an elaborate scheme orchestrated by Adam, with The Company in it with him all along...
Notice how Adam was able to walk thru walls just by touching Peter... I thought Peter absorbs other's powers, now he can give them at will too?!
Going by the paintings, it looks like Mohinder will eventually shoot HRG in the eye when he refuses to give up Claire to help Nikki out...