Board Thread:General Discussion/@comment-1913529-20160306153022/@comment-4503347-20160307053352

Based on my experience the main reason for a mission to end up in an A rank is not clearing a large number of optional enemies (e.g. weapons on ships, accompanying fighters) in Mission Update. This is particularly true with the enemy fleet in Pipeline, stealth destroyers in Tokyo, and BM carriers in Avalon. I don't know whether this is the case for you, but when it happens to me, this is usually the reason.