Ben,
Yes, the stains in your developer tray can rub off on the back of prints. It happens to me quite regularly (well, not to me, really, to my prints
).
However, these are usually just small spots that rub off fairly easily most of the time. Large, cloud-like stains would seem to indicate some other problem.
The first thing that comes to mind, of course, is fixation. Make sure you are not using exhausted fixer. Remember that fixer can go bad with age as well as with overuse, so do a quick clip-test to make sure of its activity. And, don't overuse (probably preaching to the choir here...).
Water quality could also be a problem as would HCA that is too old and has accumulated lots of contaminants.
If you tone, there could also be a problem in the toning sequence.
If your new developer tray doesn't solve the problem, post again with more details.
Best,
Doremus
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