I'll answer the question for both games.

In X they are each summoned by a random person in the Yevon Clergy because Yuna and her Guardians are branded at heretics after the incident at Bevelle. Guess that the summoners didn't get the message that they don't have to kill you anymore. Generic NCP's are usually idiots so it's no surprise.

In X-2 the despair of Shuyin Drives the fayth insane and the aeons attack as a result.

In both cases, I guess if the Aeon is called with the intent to destroy, they take the dark appearance.