I have a git superproject that references several submodules and I am trying to lock down a workflow for the rest of the my project members to work within.
For this
I had this problem with git rebase -i origin/master to a branch. I wanted to take master's version of the submodule ref, so I simply did:
git rebase -i origin/master
git reset master path/to/submodule
and then
git rebase --continue
That solved the problem for me.