When completing a CTR for an individual with more than one surname, are we suppose to place a hyphen between the 2 names?

I'm not aware of any guidance on the issue of hyphens but the examples in FinCEN's new CTR filing guidelines gives an example of two last names and they do not use a hyphen in their example, only space between the two last names. FWIW, I don't use hyphens.

I wouldn't use hyphens unless that is part of their legal name. If the individual didn't tell you it was hyphenated, I would NOT use hyphens.

A hyphen is an acceptable character if the individual uses a hyphenated name; i.e. that's what is on their identification and in the account title. However, you do not add them yourself because (on a short name) it could befoul the name control used to "match" to the TIN.