It wasn't mine anyway...
Regarding to gate station spawn problem: haven't encounter it in my playthrough. Always works as it should be for me. So made a few tests, trying to replicate. It is seems not working correctly if player's fleet is close to a planet or orbiting an object (rings or magnetic field) if it's parent body is not a primary star (like gas giants). For magnetic fields and rings orbiting a primary star works great.
So, I believe, problem is: players tries to spawn a gate right on planet (or close to it). Simple enlarging the distance from closest celestial body helps. Algorithm allow to spawn a gate in almost touching orbits, but only if different initial phase angle.
Suggestion: algorithm should stop players of building gate if it's position too close to a celestial body.
Alternate suggestion: allow gates to spawn on orbit of bodies, that are not a primary star.
P.S. real odd behavior when trying to spawn a gate right in a center of nebula system.