Yes, it’s a huge problem. The rules for AirportServices are very specific. If you miss any of the rules, the files affect all your airports. To be specific to an airport, the directory must be named AirportServices\ICAO\Services.xml or Services.spb. Being an xml or spb file isn’t a problem as far as I can tell. What really controls whether or not the Services files work appropriatel is it HAS to be specifically at this path or it affects the whole world. And the last one read in the content.xml (or wherever that data is stored now) takes precedence.
The best thing you can do is either rename the path to match the above, or delete the Services file altogether, making sure to edit the layout.json appropriately.
I have several Services.xml files from my old projects that I haven’t recompiled in a long time, and they don’t affect my world, just the airport in question.
Of course, the other problem is authors don’t read the SDK in detail and are clueless about properly writing a Services file. Then, also, improperly formed LivingWorld_cfg files can screw things up, too.