Update: After logging off for a couple hours, coming back, abandoning the mission and retaking it finally got enough commanders to spawn for me to finish the mission, but that area is definitely hinky. The fire down at that one spot that connects the north and south side of that area would appear and disappear at random. Arachnos pilons decided to do the same as one despawned into two regular Arachnos guys. That area is usually crawling with bad guys and it felt like a handful had been put in and I just happened to get them before the lot was gone. If it had just been me that ran into this, I'd think it was just something screwy for me, but several people were having the same issue.