I see the default buildings and jetways are present in my KJFK scenery.
Whenever you see duplicates items, the usual reason is a conflicting AFCAD coming from another product. Check with the free Simple Airport Scanner utility:
http://www.scruffyduck.org/simple-airport-scanner/4584282795If you have duplicated files for the airports, and remove them.
Should that not be covered by an exclude file of some sorts?
It could, and we obviously have exclude areas in the scenery.
However, there's a very well known longstanding bug in the sim, which results in certain objects (Jetways and Special effects) that would disappear from the scenery if we just made a "complete" exclude area all over the airport. In addition to that, the Autogen would disappear in a square area around the airport perimeter, with a very bad visual effect.
So, we are forced to use a very well know method of many "micro-exclude" areas, which exclude every object in the default scenery. This prevents the problem of Effects and Jetways self-excluding themselves, and the Autogen problem, but works only over the default airport so, if you have another ACAD coming from an add-on, you MUST remove it, because our exclude cannot deal with it.