I have just run a git diff, and I am getting the following output for all of my approx 10 submodules
diff --git a/.vim/bundle/bufexplorer b/.vim/bundle/bufe
A submodule may be marked as dirty if filemode settings is enabled and you changed file permissions in submodule subtree.
To disable filemode in a submodule, you can edit /.git/modules/path/to/your/submodule/config and add
[core]
filemode = false
If you want to ignore all dirty states, you can either set ignore = dirty
property in /.gitmodules file, but I think it's better to only disable filemode.