Did you see any rapid breathing in the fish before they died? I know this is a relative thing and if you don't know what is "normal", it can be tough to tell. The key is that velvet causes rapid breathing and not eating, followed by death of most fish over a couple of days. Flukes and ich kill fish much more slowly - they will continue to eat, but die over a week or two.
I noticed no rapid breathing, or I should say "abnormal change in breathing", they would get startled at first then calm down. I spend between 45 minutes and 1.5 hours per day with my QT setup. I closely observe for signs of stress or non-parasitic infection, which could require augmented treatment (e.g. Kanaplex or Metro). I pay attention to the amount they eat and what they eat to determine if they are staying nourished. I love my fish, so I admire them and count the days before they end up in my DT, where I can watch them for 16 hours a day from my desk in my home office.
I do notice the Humu Humu's were both more skiddish than any of the other fish. My Clown Trigger, which is smaller than the Humu Humu that just died, is much more bold. He is out and about. As soon as the indirect sunlight hits the tank in the morning, the Clown Trigger roams around. The Humu Humu would eventually come out but roamed less and hid under a ledge when people were about, unless it was feeding time, then he was gobbling up the mysis and the plankton. I also would drop a 5mm -ish piece of krill to allow their jaws to get a workout. Neither Humu Humu ate to the point where they got the overfilled look that is common after feeding a large quantity of food to triggers and file fish. It was just so strange to me that over the fish that were lost, they just both happened to be the exact same species.
Since starting the medicated QT process last year, I've lost several fish in QT, but there has always been a really good explanation for the loss. My fish losses during QT since November are as follows:
1) 9 Bimac anthis (a batch of 4 and another of 5), two were killed from fighting, five were lost to air bladder issues, and two never ate.
2) A Juvenile Regal Angel, killed by a much larger Blueface (my mistake, I didn't catch it in time)
3) An adult Regal Angel, never ate and had internal issues (I was extra bummed about this one)
4) Adult Majestic Angel, never ate
5) Adult Aussie Tusk, arrived upside down, recovered, ate great, died suddenly after 19 days
6) Juvi Aussie Tusk, ate great, died suddenly after about 14 days, felt like cyanide.
7) The two Humu Humu Triggers discussed in this post
I'm going to give it another show soon, and I'm going to go with a slightly larger Humu Humu (2"-3") and do the QT in my starter hotel system (two 5.5-gallon bare tanks and one 20-gallon long bare tank). That's not fully set up, but I can do one of the 5.5-gallon tanks in the guest room downstairs while I get the racks built for the hotel!