Jenkins doesn't forcibly update submodules. This means that a checkout can fail with:
hudson.plugins.git.GitException: Command "git submodule update --init --recursive modules/gmock" returned status code 1:
stderr: error: Your local changes to the following files would be overwritten by checkout:
Please, commit your changes or stash them before you can switch branches.
Unable to checkout 'ec44c6c1675c25b9827aacd08c02433cccde7780' in submodule path 'modules/gmock'
JENKINS-22510 is relevant, and cleaning the checkout before checking out would resolve the problem, that's not a viable solution. Cleaning the checkout throws away all built files, which means the build is no longer incremental.
Note, this means the behaviour for submodules doesn't match it's behaviour for the standard checkout (which is checked out with --force).