I'm not really sure i was just playing the game and it crashed mid-placing I think a conveyor? btw I have a screenshot of the original problem now.
so in this specific case i have an inserter going to a box and then another inserter taking from the box into an underground tunnel, however the second inserter isn't taking anything for some reason, it just empties the box.
P.S I have discovered that the crafting materials needed for something randomly changes, sometimes crafting a furnace costs 2 stone sometimes 10 and sometimes 5