Running apt-get update on the servers used by Ops Manager can have the sad consequence of changing the owner to the mongodb user from mongodb-mms user, potentially breaking backups for customers. The bit of code for the package that seems to apply here:
However, mongod is running as the mongodb-mms user (because Ops Manager's default user is mongodb-mms). Suggestion: chown if the directories don't previously exist, else no chown.
(opened per request of ernie.hershey)