railjack side missions having no effect?

[sunderthefirmament]

I've played a lot of railjack, and I've started to notice that side objectives don't seem to have any effect on the missions.  For example, in Corpus RJ, if Cy tells me to take out a freightlinker as a priority target, I will of course do so.  I can't start my exterminate until I do.  But even after doing that, and having Cy tell me that it has been destroyed and the Aurax troops cut off, the Corpus captain will still yammer on about sending Aurax troops from the freightlinker... the freightlinker I just destroyed.

 

It's the same thing with the autofactory side objective, and the ice mine one.  I'm not sure if destroying the cyclops array side objective has any effect or not.  But in Grineer RJ, destroying a missile platform doesn't mean the missile platform will stop shooting at your ship.

 

Are these all bugs, or are they by design?  The side objectives even change in appearance to show they've been destroyed, yet they still menace the ship.  I don't get it.