That's a tough one, because just "enforcing the behavior" isn't a good foolproof solution to the scenario you described.
You could use a blanket policy of "once it's been de-nested, it's dirty", but I imagine you would nest dirty ones on their way back to sanitation as well, and has the issue I just mentioned of not being foolproof.
I don't think the liners solves your problem, and one issue I've seen with "nested" materials in the past is that if they're stacked wet, even if clean, they'll stay wet and grow mold in storage.
My solution would be to choose one of two policies:
1. No nesting unless dirty (this way they can be nested in storage as long as they're cleaned and sanitized before use), and all nested materials will be considered "dirty" and unusable, eliminating your scenario.
2. No nesting at all.
I chose the latter for 5g buckets in my facility, either they would get stacked wet and have the problems above, or it became hard to differentiate what was clean and dirty.
QA Manager and food safety blogger in Oregon, USA.
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