Hello Nicolas,
I may have come across the same root cause, but with a control tower this time.
Below is a screenshot of LECO (A Coruña airport), the default (non-bespoke) version. In it, there is a control tower that is in the wrong position and that cannot be moved in the World Hub. The World Hub XML has a second control tower that is movable in the World Hub and is in the correct position. Is that incorrect control tower in another file, as well?
Bing Maps aerial, 43.302080, -8.381105:
Is this the same kind of issue?