So  i have destroyed all planets owned by a race next to me and taken their planets why do they still have zone of control on these systems. I have tried reloading and skipping 20 turns and nothing is it just a visual bug or what?

Same problem here.

Despite of destroying opponent their control zone is always there.

Happens also after wining the war, after truce, generally it is nearly impossible to make a system yours.

I've experienced the same thing. See attached screenshot and save game.

I'm wondering if it's anything to do with the fact that at the time of my Ground Invasion there were two colonised planets in this system. Since I had just one ground invasion for both of these planets (if this a good way, I'm not sure...), maybe the game thinks one remains under the old faction's control?

Captured system in enemy's control area.zip

I think it might be to do with how borders grow over time, as they can't decrease in size and are tied to the race. This means your borders have to outgrow their old borders to have an effect. They should be tied to the planet though, so capturing the large influence areas is possible.

I had the same thing happen in my game. Conquered Sophon homeworld and adjacent territory but their influence still extended far enough to deny me use of two asteroid belts nearby. Is this a bug or did the game designers intend for you to have to wait for your influence to outweigh all the influence you're rivals have accrued over the entire game? In theory, if you conquer the system on turn 100, it will take another 100 turns for you to build as much influence as they have. If so, that's dumb. Influence should convert to your faction when the planet is conquered. I'd understand if it were depreciated in the process, but it should flip.