I was marked incorrect for saying: "Is it a small green apple?" I thought the 'mu' word should be placed behind where the emphasis is, in this case 'small'. If the correct version is : "Is the green apple small?", should it not be written: “Yeşil elma mü kücük?” I would be very obliged if you could clarify this for me.
This cannot be "Is it a small green apple?" -- first off, that would require the adjectives to move, because they both need to come before their noun: "küçük, yeşil (bir) elma" = a small green apple.
The question particle goes after the thing being questioned, so fits perfectly fine after "küçük" if you are asking: Is the green apple (that we were talking about already) SMALL (as opposed to big)? If you said "Yeşil elma mı kücük?" you would be asking: (since we are talking about small things) Is the GREEN APPLE (among the) small (things)?
How come in this example we don't have to refer to the apple in the accusative? It was my understanding that when referring to a specific direct object 'the green apple' we use the accusative.
If we're not referring to a specific green apple, then it sounds like the question would be 'Are green apples (in general) small?'. Although as Alex mentioned below, that would require using elmalar instead of elma, which is fine.
Yeşil elma is the subject of the sentence, and you never use the accusative on the subject. The subject of the sentence is assumed to be definite and singular, unless clearly noted otherwise (bir, another determiner, plural, etc.).
Also, this is an is/are/copula sentence, so there is no direct object at all.