Well at 250k your weak attacks do between 25k and 50k damage, so it is often better to use a strong attack if the health is more than your SED. I guess you did, though, since weak attacks won't do that much damage in 6 hits. Know the feeling though, i get the same fairly often. That one attack you needed to do a X damage suddenly does X-1 resulting in the boss having a few health left.
It was a bug last event and seemingly for you now, but don't worry. It is simply a delay. You get the rewards later when you're not looking and assume they're from the ones you recently defeated instead :P