Hi Gareth,On my series 3 if the battery had been disconnected the windows did not close fully, they had to be reset.
Easy task,

Lower the window fully and keep the button pressed for 5 seconds, then raise the window fully and keep the button held for 5 seconds, that should reset the memory for the window to drop 5mm to allow the door to open without catching the hood and to raise again after the door is closed.

Hope that sorts it.
Ian


2017 Mercedes Benz SLC 200 AMG.
2019 Mercedes Benz GLA 200 AMG
Now Ex-Mogger!