I have experienced this on 3 E90's, if you want to get your window back up, click the down up button on that window a bunch of times (down then up then down then up)...might take you a min or two for it to go up, but it should. This method has worked on the last 3 E90's (Including my own still, where if I put my D/S window all the way down, it wont go up, I'm just too lazy to fix it since I never let it go all the way down...and if I do let it go down, the up down thing usually works).
It's usually never the motor, and I honestly wouldn't replace it if you don't have to because they are pretty tough compared to aftermarket. The job to replace it is around 30 mins, majority is taking the panel off and ripping back the plastic shield. There was a good how to on the forum.
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