Can you be more specific about what you're seeing? You mentioned coordinates being out of alignment. Are you talking about the numerical position values reported for each object in the editor changing? Or do you mean the objects have visibly moved within the airport? If the latter, did they move laterally, vertically, or both? Did all the objects move or only certain ones? If only some, was it limited to objects within a specific folder?
Some general notes that may be helpful:
RealFlight calculates a theoretical airport "center" based on all of the objects. As objects are added/removed/relocated, that calculation changes. The positions of objects are stored using values relative to that center. So it is normal to see those values change even if the objects are not actually moving within the scene.
If the objects are dynamic versus static (only some objects allow this), then they will move around in response to impulses or even just to settle better on the ground, particularly if they spawn slightly in the air or otherwise unbalanced. Under the right circumstances it is possible for them to "walk" around the scene little by little over time. For custom airports which are saved anew each time you exit the sim, the result can be objects shifting even if you never opened the editor.
It is not difficult to drag objects in the editor unintentionally and without even knowing it. If a whole object folder is selected at the time, then all of the objects it contains will move, not just one.
You may have simply encountered a bug with the airport editor.