Is the questioner sinful for taking a protective back cover for a phone from another phone's box, as it was not available in her original phone's box upon purchase, knowing that the phone accessories included in the box are original?

There is no sin upon you for requesting a screen protector, as you stipulated its inclusion in the contract. The fact that it was not in the original box does not affect this, for the contract is the law between the contracting parties, as Allah Almighty says: "O you who have believed, fulfill [all] contracts," and the Prophet (peace be upon him) said: "Muslims are bound by their conditions."