A lot of medications tell you to turn off your skimmer during medication. I personally am not a proponent of this practice. Without a skimmer running your oxygen levels can deplete quite rapidly to critical levels. Compound that with the stress that you are introducing with the meds themselves and you may have a bad scenario on your hands. I've noticed that sometimes fish will breath more heavily to try to get more oxygen during medication. What tends to happen is the meds you dose your tank causes the skimmer to go berserk and overflow the collection cup. If your skimmer is in sump then I would keep the skimmer on and let it overflow into the sump. As for why only some died and not all, well, if we keep with my theory and it was an oxygen issue then some fish just couldn't get enough oxygen
I'm sorry about your loss
. I've actually had this happen to me in the past too. Sucks because all you were doing is following directions.