My 5 gallon tank has been running for about 7 months now - it has live plants and one betta fish in it.
Whenever I change the water (50% once a week), all this really gross sediment and other unknown but yucky looking particles start floating around. After putting the filter back on, it'll clear within half an hour.
I do make sure I clean the gravel whenever I do a water change.
Is it in the gravel or always floating? If it's in the gravel, yes that's totally fine. All the waste falls down there and starts to get broken down. That's the point of gravel vacuuming :) Some of it will float around during a water change and will settle back down after a bit. That's fine too.