I'm guessing you're probably refering to the "Shabat Shalom" verse in "Timeless To Me", the "Good Mornigh Baltimore" reprise that Tracy and Inez sing together, the Dynamites' riff being placed after the last "Go mama go go go!" to make a scene change, and Velma's reprise of "Miss Baltimore Crabs".
They are part of the original production when it official opened on Broadway.
As for them not being on the CD that way, ask Marc Shaiman. I'm sure he knows