git-rebase + git-mergetool results in broken state

I'm experiencing an annoying issue which leaves the repository in a weird, broken state. I am attempting a rather vanilla rebase, rebasing the commits from a feature branch on top of the newest commits on master.

So, I run a typical series of commands:
1. git checkout feature-branch
2. git rebase master (conflicts ensue)
3. git mergetool

The conflicts are expected, but when using mergetool to resolve them, I encounter many "no such file or directory" errors.

mv: cannot stat ‘app/components/mediaManager/kbImageEditor.directive.coffee’: No such file or directory cp: cannot stat ‘./app/components/mediaManager/kbImageEditor.directive_BACKUP_13615.coffee’: No such file or directory mv: cannot move ‘.merge_file_ogGjXX’ to ‘./app/components/mediaManager/kbImageEditor.directive_BASE_13615.coffee’: No such file or directory /usr/lib/git-core/git-mergetool: 229: /usr/lib/git-core/git-mergetool: cannot create ./app/components/mediaManager/kbImageEditor.directive_LOCAL_13615.coffee: Directory nonexistent /usr/lib/git-core/git-mergetool: 229: /usr/lib/git-core/git-mergetool: cannot create ./app/components/mediaManager/kbImageEditor.directive_REMOTE_13615.coffee: Directory nonexistent

This leaves weird dangling files like '.merge_file_ogGjXX' in the repo, and I assume I should not proceed with the merge since it couldn't even create the files to compare.

Is this a known issue? Is there any workaround? Is it safe to proceed with the merge?

Thanks, Joe Einertson