I couldn't find anything unexpected here:

Duck had no line of sight of mex, that is why it didn't fire: a fern was blocking it with its collision volume. Would it be nice if it tried to move somewhere to attack - certainly. I'm almost certain it would have tried if it was given a direct attack command. Perhaps Maneuver move type prevent this duck to do so, not sure.

"Projectile dodging" is imperfect, but cheap. Units don't actually take into account enemy projectiles, rather just try to move in a pattern that would cause unguided rockets to miss. Sometimes it works, sometimes it doesn't.

As far as factory loss, that glaive kept shooting for like half a minute. You should have reacted yourself. Maybe if you had changed the commander move state to Roam, it would have reacted: worth testing.

Note that I used word "unexpected" in my first paragraph. Both cases with Duck and Commander are obviously not great, to say the least, but it's a behavior implemented by engine and not related to Zero-K Unit AI.