I also have a situation where muck gets stirred into the water column when I do a vac/water change, but in my case it's because I have plants and can't really get down into the substrate to vacuum so I try to gently waft stuff up with my hand towards the nozzle and invariably stuff stays in the water column for ~30min until it gets sucked into the filter. This is mostly loosened algae bits or fish/snail poop, I rarely see a flake get all the way to the ground before it gets eaten.
What I have concluded is my issue is that I run out of water that I can remove before I am satisfied with my vacuum job, so it is what it is. The rest goes into the filter but the water has particulate for ~30min after a water change.
To your original question though: fish often take stuff into their mouths to taste it, and then spit it out if it's not something they feel is edible. It could be that your fish are just sampling what's getting stirred up. If your water parameters are good and match what your fish need, and your fish are healthy and not otherwise compromised, and most importantly you don't have worms or parasite eggs in your tank, then your fish should not get sick. It's like when you get a paper cut, most often you don't get an infection in your finger because your immune system is doing it's job and combats any bacteria/viruses that might have been on the paper that you cut your finger with. Fish taste stuff often and if their immune system is working, they should not get sick from it.
thank you for the tip though, I'll try it out next time.
