When you are closing the roof and at the end the driver window or passenger window (or both) is rolled down only a bit (and the rest remain closed) It is because the anti-pitch sensor has been triggered usually because the rear window presses the front one.
It is not a problem, maybe you have to clean the rubber and lubricate them with a rubber cleaner.
If you want to open all the windows, keep holding the open-roof button when the roof has been opened.
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