Apologize for the missing item and send it along with the letter. Express gratitude for their business.
1234, Main Street
Boston, MA 02123
<Recipient Address Goes Here>
I want to apologize for the missing <missing items> in your <name of product>. I am sending you the <missing items> and hope that you will forgive our oversight.
We appreciate your understanding and hope you enjoy your <name of product>.
encl: <List of enclosed items goes here>