Transfer Rate Limit?

Does GitLab apply some kind of rate transfer limit to cloning, pushing, or pulling operations?

The speeds I’m seeing are random, and some of my users are experiencing slow speeds during certain parts of the day and then faster speeds during others. I don’t think this server is serving up that much traffic…

No. GitLab does not apply a rate transfer limit on any operation.

As from GitLab 8.4, GitLab has a performance monitoring system available for both CE and EE; see: http://doc.gitlab.com/ce/monitoring/performance/introduction.html. This would help you to gather some more data to help in the investigation.

Note that you may also need to check on your network speed both to the client and to the server, disk IO on your server etc