Agreed the game needs true borders, and then a separate field of influence. 

Confirm that, please find the below save game for analysis:

https://www.dropbox.com/s/gjxglezh6e8rz8y/05%20Terran%20Core.GC3Sav?dl=0

Description for save game:

• Notice the large amount of ships next to my planets by a friendly as can be "Altarian Empire"
• Said friendly CIV is in war with the  "Iconians" who also happen to be friends of mine.
• My CIV was never in war with any of them, still the Altarian Empire stages ships in my territory instead of moving against the Iconians right next door. Is it afraid I might back them up?
• Also need to add, I did take over 2 of the Altarian Empires planets via friendly acquisition of culture - is that the reason they are acting up?
• They also have a large amount of star bases in my territory - are they defending those? If yes, then why are they staging ships also next to planets of mine that do not have any star-bases near to them?
• Noticed this same behavior with another CIV east from me in the first half of the game, but destroyed them meanwhile so it is not visible anymore (their large amount of fleets next to my planets was making me itchy - they could have benefited from a diplomacy warning from my side: move out or face the consequences)
• Also notice a similar behavior  from the Thalans and Vogrons on the east side of my territory though not that visible yet

At first I though it might be something special in the specific game but if this is a generic occurrence it might need to be fixed

Yes it is extremely annoying to the point that I want to declare war just to clean up their ships in my ZOC but I then have to place a ship right next to every one of theirs in order to stop them from wiping out all my shipyards because that's where the dicks all park. 

When I play with a lot of factions, it is at the point that my kids stand by me while I play. They love it... because it it full of colors. 

"Let me recap.  I've laid waste to the enemy defenses, moved transports into position, complete with defending fleets that their enemy cannot possibly destroy, and given them the keys... and they do nothing."

Is it possible that this particular faction as a hight diplomatic priority, at the point that they do not plan to invade anyone?

Question to all of you.

Did all of you, use the rally Points in Your game ?, when the AL ships parkin/gather at Your Territory near (shipyards,rally-Points,and around clusters of Your ships.)

if so then there is a bug when you use rally Points.

(might be the possible bug, but just one out of many theories)

I did not use rally points either.

The same thing is happening to me in the current game, and this is actually the first time that it has happened. I am still in 1.3, but I did not have this problem until now.

Pretty much every race that is in travel range of my Z0C is just parking about half of their fleet there. A few of them, like the Yor and Drengin were furious with me early on, but now that I have enough diplomatic points to be close to every race, they are not moving their ships at all. It is annoying because they are getting in the way of me building star bases simply because they are so cluttered.

Like some have mentioned, even though said races have wars going on, their ships are still just sitting there. To the northeast of my ZoC, the Yor and Iconians are going at it, but half of the Yor's fleet is just hanging around in my yard. It could be because the Yor are at like...-700K credits, but then then they are still fighting.

In previous games, the factions usually pulled back all of their ships once we are at peace, but this time it is just broken.

Hows that for an interstellar parking lot? I count at least 6 other races within that section of my borders. None of them are at war with me, or with the others shown in this pic, however most of them are at war with someone else and usually far away from that location.

I'm Red by the way. Oddly enough, Light Purple, who has the MOST ships in that area, is actually the least interested party, its space is by far the furthest away from that location Its a bit confusing because there are 3 shades of purple, but the lighter purple is pictured in the minimap in the upper left hand corner, that is the closest their space is to mine and they have to cross almost 3 other empires space to park in my lot. Guess I have the best rates?

Nope, tried it. It's definitely interested in parking military ships in your influence. And just parking them, not much else. 

I am experiencing this as well. It is extremely annoying and it is lagging the game as well, due to sheer number of ships in small space.

Has it been adressed with the newest 27/10 update?

No this has not been addressed, I am 240 turns into a 1.4 game on incredible/genius mix difficulty map size just under insane as a custom faction. All the AI do it to me still and I find myself setting up fleets next to every one of theirs and declaring war for the sole purpose of cleaning up the damn ships throughout my zoc lol.

Yeah, this is definitely alive and well in 1.4.

Next up, the AI is ignoring game settings, such as "no tech trading", "no surrender", and the game's interface is ignoring "show all ships" options.

Also, my system is back to chugging hard past turn 250.

*sigh*.