Though support say otherwise, it might be working as intended. If you previously gained a bounty for e.g. reckless flying or hitting something clean in the now fire zone, the station shot the player down.
Due to the station guns upgrade, the shooting down and bounty issuing happens now at the same time.
If the mechanic stays the same for carrying wanted passengers (getting scanned near the station=bounty=station kill), player need to be careful about selecting the passengers. Wanted passengers should not be transported by Liners, they should be smuggled on-board small ships, like the infamous Cobra MKIII.
The missions for transporting criminals are well-payed, considering the fact, that they usually only require a class 4 economy cabin, which can be fit on several small ships.
What needs some improvement, is the game warning the player about a wanted passenger, as it currently requires careful reading of one hint in several lines of mission description. Especially with HUD color changes, the hint in warning color might be harder to see/read than the rest of the text.