It is possible that one piece of trash glitched out and clipped through the map. It's also possible that there is clutter that is hanging on a wall such as cobwebs or something that you missed. I remember that in one level there was a flag hanging above the tracks that I could never find because I only looked at the ground.

If it is a train car, it could be glass, double check the windows and make sure they are all fixed. Check under the train in case something rolled under it. Also check around the train as the item may not even be in the train.

Worse case you may have to restart the level. I know that sucks but I have had to restart levels on more than one occasion.