"Is he eating the soup with a fork?"
Translation:Czy on je zupę widelcem?
I'm not great with syntax, but I think the object (the direct object) is the soup... basically, the fork is "the instrument", so it takes Instrumental :)
I think fork is in instrumental because it is preceded by 'we' which doesn't need to be translated separately.
Yes, it would have the nonsensical meaning where the fork is eating as well.
Also, you have a typo, it's "widelec", but "widelcem". I remember that used to be a mistake in the Wiktionary declension table, but it's been fixed.