* Spoiling introduced the concept of an item in an inserter hand changing as the inserter was swinging to the destination.
* Since the inserter hand contents may change while it's on the way to the target, it needed a way to get rid of the result item once it got to the target instead of getting stuck forever
* Burner fuel sources have a "trash" inventory where items that spoil, or produce burnt-result go
* Items in the burnt result inventory of the burner fuel inventory will get extracted from the burner when inserters go to grab anything from the entity
* If an inserter is bringing something to an entity and the item doesn't fit into the entity when it gets there, and the item is marked as "produced by spoiling" it is put into the entity trash inventory for later disposal
* Since copper ore is a result of an item spoiling it is considered a "trash result" item and the inserter when it tries to put it into the locomotive ends up putting it into the trash inventory since it won't fit in other places
Everything is working as intended, however the result is not desired. I have no solutions to stop inserters from doing that since generically they're working correctly from everything the game engine knows about.
If you want to get ahold of me I'm almost always on Discord.