A check for loan proceeds (drawn on our bank) was payable to husband and wife and the husband endorsed the check and the wife cashed most of the check, opening a new account in her name with the remainder. The cash was given to the wife, the husband had left. I completed the CTR in her name only, but then questioned myself. Isn't that right since he didn't physically receive the cash at the teller window?

But wasn't it made payable in both their names, therefore making it also on his behalf.....

Well, that's why I started questioning it. I haven't sent it in yet. I should have his information though.

The paper "evidence" suggests that the transaction was on behalf of both payees. Whether you file with two Section A entries or one should depend on whether you got other information that leads you to believe it was done only on behalf of the wife (more, I think, than the mere fact he didn't directly receive any cash).