User blog comment:IamJakuhoRaikoben/Chapter 415: And It Shall Become Your Will To Live, Review./@comment-7418318-20150112233703/@comment-7418318-20150115092734

Or maybe he was in love with a female Dragon Slayer. The pro-Human faction saw that a particular battle was lost and had to retreat. A small group of Slayers and Dragons was either left behind or volunteered to stay behind to cover the escape of the lager force and were ultimately annihilated.

Acnologia in his grief felt like the loyal Dragons betrayed his love-interest and went crazy as a result, slauthering Dragons regardless of faction.

Could be possible too.