It sounds like you're suggesting that it's the ATM owner's responsibility to monitor and report CTRs when they aggregate over $10,000?
If your customer withdrew $11,000 from another bank by cashing a check, that's the other bank's responsibility to report. If your customer withdrew $10,000 from them then walked to the ATM in their lobby and took out $200, I'm certain there are very few banks if any that would report it, because they don't have the relevant information. Only the bank that owns the account can say whose card that was, and they were identified as the conductor of the transaction because of that bank's PIN.
Anyway, if these transactions appear on a cash report or are otherwise indicated to be cash in your system, I think you need to make a very clear explanation for why you don't either believe them to be cash or think that it's your responsibility to monitor, and hope that your examiner agrees.
If this was our customer, we'd complete the CTR.