@JennyWondracek 

When you enroll the students in their own sections, are you setting their enrollment so that it is limited to only interact with users in their own section?  According to the documentation, this setting also affects Conversations.  Thus, if they are each enrolled in their own section, they shouldn't be able message each other when they are in different sections and their interactions are limited to their own section.  How do I limit a user to only interact with other users in the same course section?