Here's the symptom:
$ git clone https://github.com/polydawn/refmt
$ cd refmt
$ git submodule update --init
...
fatal: clone of 'https://github.com/go-yaml/yaml/' into submodule path '/Users/dkegel/src/refmt/.gopath/src/github.com/go-yaml/yaml' failed
fatal: clone of 'https://github.com/urfave/cli/' into submodule path '/Users/dkegel/src/refmt/.gopath/src/github.com/urfave/cli' failed
The fix is to remove the trailing slashes on those two lines in .gitmodules.