are we supposed to obtain the items when they're collected with the debugging tool?
I can't do any upgrades because nothing is going in my collection
Yes, because of the bug, they can be obtained through the debugging tool.
I would suggest you to use the random looting from the warehouse to get the materials.
I will fix that and upload a new update for this jam: https://itch.io/jam/improve-my-game-jam-23