The auto up mechanism has a safety feature that is designed to stop & reverse if it senses an obstacle - if the window mechanism has been disassembled, the auto feature needs to be reset after reassembly so that it knows where the top of the window is - you'll find the instructions to do this in the service manual in the resource section of the forum.
Can I assume ...
your car has "auto up" on that window?
The auto up mechanism has a safety feature that is designed to stop & reverse if it senses an obstacle - if the window mechanism has been disassembled, the auto feature needs to be reset after reassembly so that it knows where the top of the window is - you'll find the instructions to do this in the service manual in the resource section of the forum.