It has always worked like that for me. If I go into the editor and edit the position of a vehicle or something and then press Y to exit, the apply button is never enabled when I get back to that screen.
What I do is check (or uncheck, if it is already checked) the "Disable staircases" option. As soon as I click the box, the apply button becomes enabled. I click on the checkbox again to put it where it was and then click apply.
However, it does seem that the edited positions get saved if you just press Y after you have adjusted the positions and then close the dialog box. I just do the staircase thing because it feels better to me to have clicked apply.