If you use sudo for commands like docker run, remember that your environment variables will not be transferred to the sudo environment. You can set environment variables for sudo commands like this.
sudo DOCKER_HOST=localhost:2377 docker run -td -e CALICO_IP=192.168.100.1 busybox
If you see this exception, it means calicoctl can't communicate with your etcd cluster. Ensure etcd is up and listening on localhost:4001
Running ip route shows what routes have been programmed. Routes from other hosts should show that they are programmed by bird.
If your hosts reboot themselves with a message from locksmithd your cached CoreOS image is out of date. Use vagrant box update to pull the new version. I recommend doing a vagrant destroy; vagrant up to start from a clean slate afterwards.
If you hit issues, please raise tickets. Diags can be collected and easily uploaded with the sudo ./calicoctl diags --upload command.