I said "Julia eats from a spoon" and this was incorrect, why?
I think it's just because they haven't added it as an alternate translation yet. You can report it if you see it again.
Nope. Julia eats with the plates, cutlery and hands
Is there a reason one says चम्मच से and not चम्मच के साथ? Or are both correct?
You use से when 'with' means 'using' and 'के साथ' when it means 'accompanied by'.