An enemy can get stuck in the ghost hacking area, causing the objective counter not to progress. In my case, it was a thrall with the caltrops bane, getting stuck in a spawn door. The door was the one next to a tanker truck, where thrall and 2 wizards spawn at the start of phase 2/3.
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Caltrops Bane enemies seem to get stuck in spawning doors frequently. It's like their "chase down the player constantly" movement code clashes with their "run out of the spawner" initial animation and completely breaks their pathing logic so they stop moving. This goes double if that Caltrops Bane enemy is a flying enemy. I hardly ever see them move from their initial spawn point.