I would do a risk assessment based on a points system you average at the end.
For example, here are some questions you can ask and the corresponding point system:
Low risk 1 - 4 points
Medium risk 5-7 points
High Risk 8 - 10 points
Questions:
1. Are finished products in tamper-evident containers? (all = low maybe a 1 this should be your answer if you're manufacturing foods/dietary supplements)
2. Are finished products stored in a separate area from raw materials? (yes = low risk, maybe a 1), (most = medium risk, maybe a 6), (finished product is stored all throughout the warehouse next to other goods = high)
3. Are finished product pallets shrink-wrapped or have an additional protective barrier? (yes, maybe a 1), (no = medium risk)
4. Are conditions in the warehouse cleaned and organized?
5. Pull staff training records and review if they have proper job training (all are trained, less than 1)
6. (extra credit) make a competency quick for the warehouse staff.
Tally all the results, average them out, and figure if everything is low, medium, or high risk.
There are many other questions you can ask and things you can add to the risk assessment.
At the end, make sure you have a root cause section if something is medium or high risk, also, have a preventive measure section discussing what you will do to prevent cross-contamination.
Use this at your own risk, I am not responsible for your audit or audit grades.
