Does the alif in His — Exalted be He — saying: (So they found a servant from among Our servants to whom We had granted mercy from Us) refer to Moses alone, or to him and his young companion?

The "alif" in the Almighty's saying: (They found a servant from among Our servants) is the alif of duality (alif al-ithnayn) which refers to Musa and his servant, as is clear from the preceding verses (they reached, they forgot, they passed beyond, they returned) which refer to both of them. If the pronoun referred to Musa alone, it would have been said "he found."