That happens to me, too, but as soon as I leave the area it gets corrupted again

This is a recent bug (late 3.95 or 3.96).

Oh no please no border gore in my GC3 *shudder

I have the same problem. I play with the game option: No FOW in your territory set to On (default). The fow in the area corresponding to the zone of influence is not updated correctly.
A save file to show the problem is useless in this case, because when we load a save file the fow is updated correctly, it is only during the game that it does not work properly.

Retribution v3.96, standard races, all expansions and DLCs, no mods.

The fow is not removed correctly during game:





And yes, I also noticed the bug with the ships that make holes in the fow.

Hi Rap you do understand that influence is determined by your planets, and starrbases, not just your planets. Even, if it was just your planets they are not evenly spaced apart. 

Now as far as the fow I think it does it one space from the edge of you influence border. I've noticed this problem to.

I certainly do. The problem is not with the planet's influence but with the FoW influence. This is what seems to be corrupted right now. Nice hexes should be the case and not these strange, blocky shapes that are now showing up. See the previous examples provided by other posters' images and you'll see what I mean.