What you are seeing on your debris tray is not actually rust, but a natural chemical reaction that is occurring.
As your little bot swims through your pool catching all the pesky debris she is also collecting a build-up from the minerals that naturally occur in your water.
The build-up occurs on the mesh screen and causes a chemical reaction with the coating on the stainless steel mesh resulting in what looks like rust.
Don't worry the chemical reaction is perfectly natural and is not a sign of anything wrong with your pool water.
We know that the spots look icky, but if you will use either a very diluted solution of CLR or a mildly diluted solution of vinegar and a soft-bristled brush, (we recommend a toothbrush), they will clean right off.
So can we stop this from occurring?
The short answer is we are working on it.
We have experimented with other materials for our filter but have not found anything that is as durable as the stainless steel mesh we currently use.
We are continuing to investigate other options to find one that is more maintenance free for our little bot owners but until we find that magic combination your debris tray may need a little TLC from time to time.