I just opened four Atlas O Gunderson 53' Well cars and three sets had loose plastic wedge guides that came off the metal car bodies. Two were on the side of two separate cars and two were at the end of a well. The end wedge guides were originally glued out of place preventing the 53' Container from going into the BNSF well. Of the twelve wells on my four sets, only one had this problem that prevented the container from seating itself properly. A little glue will reattach the wedge guide that aides workers in aligning the container as it is lowered into the car.
WATCH FOR LOOSE PARTS when you open your well car sets. The plastic to metal bond can come loose. There is a little notch on the side of the car that will help align the part when it is glued back in place.
I also glued my small pins into the BOTTOM of my containers. Gluing them in the BOTTOM prevents marking or scarring the roof of the containers. You might want to rotate the containers up and down to give the train a new look. The pins on the BOTTOM will allow this.
Guide the door latch side of the container down into the well first, but not at too steep an angle that prevents the container from dropping into place. Putting the door latch side in first will help reduce the breaking off of the door detail parts.
Here are some pictures.
John Rowlen, "Valley of Bridges"