Sounds like you need to recalibrate the window, this happened to me recently I tried this:
1. Engage the auto-down function and
remove fuse 11C/5 (for driver's side) or 11C/4 (for passenger side) (located in the driver's side dash fusebox)
during window movement.
2. Install fuse back into position.
3. Engage the auto-up function and hold it engaged for 5 seconds after the window has reached the fully closed position.
4. Verify window is now working properly.
5. If this procedure does not work, a scan tool that can access the Passenger Door Module (PDM) and Drivers Door Module (DDM) will be needed.
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The auto up or down function will be engaged if the button is pulled to the second step. The first step is for manual operation. This procedure can be used for driver and passenger windows.
More info
here