I leave my canister on when I do water changes and it really doesn't pose a problem. Only time i turn it off is when i do the maintenance on the filter obviously. when you see the fish waste and debris coming out of the output nozzles after you turn on the filter, that's the tank water that was stuck in the ribbed hosing that didn't go through the filter and the media. you can think of it as "back wash"
it's actually a good sign, because now you know your filter is "grabbing" the waste and is doing it's job
it's actually a good sign, because now you know your filter is "grabbing" the waste and is doing it's job