I don't know if I'm doing it wrong or I formatted it wrong but when I try to add a block or item to the list, it does not work it only blocks the default item there (the shield) even with the added items. I format it like this:

disable-crafting:
Disable the crafting of specified items
enabled: true
worlds: ["Factions"]
List of denied items
denied: [shield,hopper,golden_apple:1]

(Do I need quotation marks or something like this "[item]" or this '[item]'?

You should not have quotation marks around "Factions"