Agents receive a banana to signal that they are the killer's next victim. When Agent Roberts is seen opening his banana, Agent Armstrong is already knocking on the door, and immediately reports that CONTROL has numerous agents deployed. However, they shouldn't have known he was next until he received the banana.
The Chief states that six (later seven) agents have been killed by the banana murderer. All of them must have been guarded by Agent Armstrong, as he's the killer. However, it's unlikely that a real intelligence agency would repeatedly assign the same agent to serve as bodyguard, particularly if he failed to protect his charge. Indeed, one murder on his watch would almost certainly result in him being placed on leave pending an investigation, and two would result in dismissal. Further, a rookie agent would be an unlikely choice to head such an important assignment.
When the Chief and Larabee arrest Dr. Rath at the end, his equipment that controls the ape is to the left of the room. They should have used the equipment to make the ape become Armstrong again and not hurt 99. That way Max would not have had to fight him and 99 wouldn't have been in danger longer than what she should have been.