So game after scrapping updates but doesn’t save inventory status and when you enter manufacturing screen with link from personnel screen it restores previous inventory state while you still have resources from that scrapping. Nice catch.
If you scrap an item on a soldier then it also updates the inventory state so the bug doesn’t occur.
I have confirmed it seems to happen when scrapping stuff from your stores and then going to manufacture something and escaping.
Edit: If you look when scrapping from the stores, your storage value (i.e. Storage 100/200) doesn’t change when scrapping. I think this is an indication it doesn’t update immediately.