We have a relationship with a customer who is husband and wife - they are the managing members of an LLC. She withdrew $9,300 from their personal account and at the same time withdrew $1,100 from their LLC account (which operates under a seperate EIN). She received all the funds at the same time. Should a CTR be filed?

Since a single individual received more than $10,000, yes, a CTR is required.

And that would be true whether the withdrawal from the LLC was completed on behalf of the LLC or on her behalf. The deciding factor for filing is that the transactions were both completed by the same individual on the same business day.