In the legion mission, I have selected the task "Capture Vortex Entities." So far, I have disabled 2 of them in my battle tab, but the progress hasn't showed up yet for either of them. (It still shows 0). I have done this mission before with no problems, but had I known about this bug I would have selected another task.

Doesn't that mission give you an artifact to use on them before disabling? Did you do that?

It does and he probably didn't.

You have to remove the shields from the enemy, use the item which gives you progress in the mission then you kill it.