That normally happens when a door skin has been replaced and the forming of the skin did not move that flange inside the window slot down far enough.   It can also happen with an original door, but not as likely.  It even happened on OverHaulin once and they did not know how to fix it.

To fix it, remove the rubber stop at the bottom of the door.  The one that stops the window's travel downward.  That will get the top of the glass below that flange.

Then, stand outside the car door and, with your fingers, go along that flange and bend it down and towards you.  It won't take much force to bend it, and does not require you to move it very far.

Once you bend it a little, roll up the window and it should clear.  Then replace the rubber stop inside the door.

Better revisit everything you did when you adjusted it as well, then.

It looks like an arrow head that presses thru a slot and locks into place . If it is the original and hard it will be difficult to get out without breaking. Put some lube on it and twist and pull up trying to get one end to start comeing out. If you get it started it will come out. If you get it out with out breaking it, it should go back in without a lot of bad words.  If you have to put a new one in Good luck.

I use a screwdriver to push in the rubber right next to the slot in the metal holder, Works well for me.
Howard