I noticed something similar the other day when playing around with xdotool. I asked it where a window was and then moved the window to that position - what should have been a no-op - and the window moved. I figured it was an interaction with the Cinnamon window manager. Yours (if not Cinnamon) may be doing the same.
xdotool reports where it "thinks" a window is. Requesting where a window be moved with xdotool is handed off to the window manager, which may or may not take into account window spacing, borders, the phase of the moon, etc., and so that might put the window in a slightly different place.
You could try wmctrl instead. It's not as feature rich, but can definitely move windows around and might have different results for you. (I know I use it for one thing in particular and that seems to work, but then it has been a while since I set it up and I can easily imagine having tweaked the numbers until things looked right.)
There's also that some software really doesn't like to be moved or resized and will refuse to change. That's bad practice, but there's nothing that can be done really, unless you have an especially forceful window manager.