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Sounds like the myths got mixed up. I asked around at another forum about mythology, and some people responded that they might have gotten a few of the myths mixed up. Here's what one guy posted.
From Wikipedia:
Trojan War
Apollo shot arrows infected with the plague into the Greek encampment during the Trojan War in retribution for Agamemnon's insult to Chryses, a priest of Apollo whose daughter Chryseis had been captured. He demanded her return, and the Achaeans complied, indirectly causing the anger of Achilles, which is the theme of the Iliad.
When Diomedes injured Aeneas (Iliad), Apollo rescued him. First, Aphrodite tried to rescue Aeneas but Diomedes injured her as well. Aeneas was then enveloped in a cloud by Apollo, who took him to Pergamos, a sacred spot in Troy.
Apollo aided Paris in the killing of Achilles by guiding the arrow of his bow into Achilles' heel. One interpretation of his motive is that it was in revenge for Achilles' sacrilege in murdering Troilus, the god's own son by Hecuba, on the very altar of the god's own temple.
He's probably getting the myths mixed up with when Apollo was shot by Eros's arrow and fell in love with Daphne.
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