Translation:She has an apple, but it is green.
I take this sentence as clarifying that she in fact has an apple, only not the color that was expected by the interlocutor; hence the use of the conjunction αλλά. On the other hand, when a Spanish speaker states that a certain fruit is green, it means that said fruit is not yet ripe for eating. (El mango está verde./The mango is not yet ripe.) Is that also the case in Greek?
The word μήλο is of neuter gender and adjectives describing it must also be neuter, so you have to use πράσινο. If you used πράσινη, which is the feminine form, then the reader of the sentence "Αυτή έχει ένα μήλο, αλλά είναι πράσινη" would understand "she has an apple, but she is green" which makes no sense.