Who/what was controlling the killer robot before Wikus got in?

Yes you missed the scene where Christopher's son activated the killer robot which is actually a battle suit.

As it is clear from the following wiki plot lines

Christopher's son activates the mothership and an alien mechanized battle suit which saves Wikus by killing Obesandjo and his men. Wikus takes control of the battle suit and rescues Christopher

Immediately before Wikus gets in the alien battle mech "suit," there is no indication that anyone is controlling the mech. So the mech appears to autonomously and efficiently defend itself: halting and collecting (with some sort of force field) the hail of bullets fired at it, and then discharging the ball of bullets back at the humans who had fired them.

Given how effective the mech is at defending itself, the question becomes: "Why did the mech become vulnerable to bullets once Wikus was operating it?" With Wikus at the controls the mech was finally destroyed by accumulated damage from bullets (and one RPG).

Other than for dramatic effect, this plot point seems consistent with the theme that Wikus is an incompetent boob who can and will screw up anything.