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Sometimes dead fish are sucked toward the filter intake, so he may have died in another way and that's where you found him. You can cover your filter intake with a prefilter sponge. I have them on all my filter intakes because I keep shrimp in my tanks. If you feel like your filter is too strong, you should also be able to limit the flow some.
 

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Smaller danios are not very strong swimmers, even more so the long fin varieties.
I have lost quite few to my hob filter before realising it. Some were small enough (half adult size) to make it through the aquaclear's intake grid and they would live inside the hob 'til rediscovery.
Even with foam on, it would still happen. Once they are fully grown they can manage the current.
 
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