It is not a mystery anymore. In Iron Man 2, we have seen the Russian physicist made such Iron Man suits which can't be operated from inside. remember how agent Rhodes got confined in that suit and he could not leave it. The villain in this movie who held the president captive is a scientist himself. As we saw, at the end of Iron Man 2, the suit was retained by the United States Govt. which Rhodes took away, it is presumable no new upgradation has been done to it (_at least not shown_). So the suit still remain vulnerable and as @Avner rightly commented possibly the villain got the equipment to control the  suit, connected to the suit during the upgradation by AIM.