Whenever I shut off my filter when I clean, a certain amount of particulate (a nice way of saying YUCK) comes out and floats around. I like to unplug it before I have vacumned out the allotment of water so I can suck up the majority of the stuff. It gets filtered out right away as soon as the filter gets turned back on.
I think a certain amount of stuff is not stuck to the filter pads, or has not gone through the strainer grate in the filter. The force of the water is holding it in the filter. When the water is no longer passing through the filter and falls back into the tank from the filter, all the stuff that is not stuck comes with the water.
It is normal enough - suck what you can out and the rest will get filtered.