Welcome to the E46 Design Flaws.
It is most likely related to the window regulator itself. There are a lot of plastic in the regulator, and it is of very poor quality.
I compared the E46 with a Hyundai Accent one, and I think the Hyundai one is stronger.
It's that bad. It doesn't align well from the Factory.
The ebay ones are of the same quality as the factory ones. I bought all 4 just in case back in the day.
Even after one warranty replacement of a regulator, I think I used 3 out of the 4 that I bought as spares.
For now, you should open the door panel up, and push the window up. Depending on what is broken, I would put a screw/bolt in the regulator to hold the glass up.
There are several DIY's...
Also.. buy some Rust proofing, and spray the inside of the door.
E46's rust from the inside out. You might as well spray the inside of the door seams while you have the chance.