But at most airport the numbers published e.g. at navigraph charts does not match up with GSX.
GSX is not making up data or reads data from somewhere internal to it. GSX obtains data from the simulator itself, making a standard call to the Simconnet Navdata API so, what you'll see in GSX, will be exactly what the simulator is seeing, good or bad.
If a scenery doesn't match current aviation data, it's only a problem caused by whoever made the scenery, GSX has no effect on that, it will just use what's in the simulator already.
That's because you reported "GSX" doesn't match navigraph charts ( when in fact it was the sim not matching it ).
If, instead, you notice you see some parking spots in the World Map in the sim, and those are
different than what you have in GSX, than it's a completely different issue, and might possibly indicate conflicting sceneries installer.