Ah, I had that once, too. In fact, I had 199 darwinians, so one was missing.
A few of them were still outside one was continuously encircling an incubator, three had somehow got out of the shield and were now trapped between shield and water. None of then would follow the orders of an officer, they completely ignored it.
Too bad there is no way to convert an officer back to a standard Darwinian without killing it.
On second try, I had almost 300 darwinians. I'd suggest that you get the doc to work on the program manager, so you can run more programs simultaneously, or the engineers, so they can carry more souls at once.
You can create engineers near your squad, so you should do that when you kill virus. The engineers will immediately start to collect souls. If there's an incubator nearby, they'll bring it there, if not, they'll just carry them.
Just be careful to keep their path clear. I never managed to hit one with my lasers, but don't use grenades when they're nearby.