Yeah, dragonfly nymphs are very efficient hunters and prey on small fishes and invertebrates. Best to remove them as soon as possible.
Soil substrates will naturally tend to trap a layer of organic waste and mulm, which is okay as rooted plants will usually help to use the nutrients that are generated. But a good filter with ample circulation will be able to push the mulm and waste into its intake and trap most of it in the filter media (which you then proceed to rinse and clean regularly).
A filter with higher flow can help... more importantly, the flow should be able to move water all around the tank, not just at one area. Hang-on filters tend to be rather limited in their outflow path, so maybe consider a mini canister filter with intakes and outflows that can be adjusted to create good tank-wide circulation.
If your current filter media or sponges have large pores, all the fine dirt and waste material will just keep flowing back into the tank, so adding fine white filter wool into the filter will enable it to trap the dirt and debris, which in turn helps to keep the tank cleaner. Note that you do have to change the fine white filter wool regularly as it will gradually clog up and slow down the flow.
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