well I know you need rounded corners in bait holders so they don't get stressed out feeling trapped in corners and if you put too many in, they die from overcrowding, so if your good on those issues I would say you don't have enough oxygen in the water for them and you need add some more air pumps and bubblers to it. if your bait containers have corners then put a bubbler in each corner so the bubbles act as to make a rounded corners so the fish don't stack up there.
shrimp will actually fight and kill each other with their horns if they are bumping into each other and as things die they spoil the water so try a constant water flow system that continuously brings in fresh water and overflows out the old water.
most bait dying issues are from overcrowding causing low oxygen or the shrimp horning other bait if they are mixed
your problem might just simply be you are trying to have too much bait for the size of your container
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