It looks like if I run sudo docker-compose start after boot, the remaining containers that didn't auto-start will spin up. I am not seeing anything in the docker-compose.yml file that stands out that wouldn't start specific containers.
The permissions are correct on the mongo repository. These permissions were not changed, as I followed the instructions on github, with cloning the repo via git (not downloading with a browser), and running ./setup & ./start, which run provided scripts by Netskope. The only reason I ran docker-compose was due to the issue with RabbitMQ starting after reboot.
Working with someone at Netskope last week, they verified this is an issue and he put a ticket in to get this resolved. Also moving to 3.3 doesn't resolve the issue.