The problem is that you're putting a <<set>> macro inside of a Twine link, which won't work. Try this instead:
"Here, you can have some rations if you wish?"
[[Take the Items and thank the Master Chief|Extra Rations Exit][$score += 3, $playerInventory.rations = { name: "Rations", quantity: 2, weight: 1.0, description: "''@@.item;Provisions for nourishment and sustenance. Not the tastiest, but long-lasting and filling enough.@@''" }]]
[[Refuse the Items|No Extra Rations Exit][$score += 8]]
To put that in a bit more readable form, you can have multiple expressions (such as "$score += 3") if you separate them by commas like this:
[[Link text|Passage name][expression, expression]]
Hope that helps! :-)