One person who works for the owner of two separate businesses makes a deposit into both businesses.
CTR rules require that deposits be aggregated if they are BY or ON BEHALF OF the same person. Did the one individual who made deposits to both business accounts individually bring in more than 10k? If the answer is yes, then you must aggregate. If the answer is no, then you do not.
Example:
Transactor 1 - Deposits $6000 to Business A and $6000 to Business B
Transactor 2 Deposits $3000 to Business A
Transactor 3 Deposits $3000 to Business A
In this example since Transactor 1 brought in $12000, the deposit to Business B is included in the CTR.
Example 2:
Transactor 1 Deposits $3000 to Business A and $3000 to business B
Transactor 2 Deposits $5000 to Business A
Transactor 3 Deposits $4000 to Business A
In this case, no single person brought in more than $10k, but Business A benefited from $12000 so your CTR would only include deposits to Business A.