The ideal position for the window frame is with the rubber surround just touching the door frame so it makes a seal but isn't jammed up against it. I've noticed its quite common for the top corner of the seal to drop slightly - presumably because the rubber has shrunk over time. This leaves a few mm gap at the top which can cause a bit of wind noise. I've not investigating fixing it yet but I think it'll need the whole window frame removing and the seal repositioning.
There are also rubber seals on the leading edge of the door skins to seal off turbulent air. You can get a bit of noise if one of those is missing.
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