I have seen this twice myself and at least once in streams. So far it comes in one of two flavors:
1. If the next item to go into a building on a conveyor isn't wanted the easiest way to clear it out is to disassemble the conveyor and rebuild it. I have been able to select the item but it's rare, most of the time you select the building. Happened to me with loading the space elevator and saw a stream when someone changed a smelter and missed the last piece of ore.
2. If you drop an item on a resource node you only get the option to mine the node and not to pick up the item. This happened only once to me early on when trying to figure out how to eat berries. I dropped it and lost it forever because I could not pick it up.
I would love to see a key or toggle that ignored everything expect items for targeting.