Chipmonk
My Family has had a pond for 40 years. When we were kids we stocked the pond with Bluegills, crapie, perch and bass. The fish thrived in the pond for many years, untill a couple of years ago. One day all the fish in the pond were dead. We did a lot of research as to why this happened. The only thing that we came up with is lack of oxygen. Its something that can happen on hot summer days with cloud cover, and its caused by dying plant life. When sunlight is blocked by snow and ice cover or clouds, photosynthesis is reduced, which is a biologic process during which plant life releases oxygen. Plant and leaf litter decay robs oxygen from the water.
There was always at differant times algie on the pond and we would kill it with a diluted coper-sulfate and water mixture. This never had killed a fish. A few years ago a plant life called duck weed was introduced to the pond. Its a lime green plant life that compleatly covers the pond. It was introduced from chicken manure pellets being spread on a field near the pond. We think that the duck weed contributed to the lack of oxygen in the pond that killed the fish. We are in the process of killing the duck weed which is kind of costly.
Maybe your ponds have a low amount of oxygen, and when the minnows are confined to a trap thier movement is liminted, in turn are not able to get enough oxygen from the water by moveing around. I'm not sure if this is the cause, just a guess. If you wanted to know for sure you could place a small aerator under your trap. If they still come up dead, its something else thats killing them.