I have it set where the chest should only spawn 4 items, but every once in a while it'll spawn 6. I also have a custom item list to spawn in the chests, but every once in a while it'll spawn items that aren't on the list. Once it spawned 1500 scrap and I don't even have any scrap that is supposed to spawn in them.

It's accurate. The reason this happens is because events can spawn on top of barrels or crates. When this happens the barrel or crate items are merged into the chest rather than deleted. 

How would it get 1500 scrap in the box then? lol

When this happens the barrel or crate items are merged into the chest rather than deleted.