I also blocked with this issue on my project. After googling for 2 days I realized this issue was from Xcode 5, was fixed (or maybe not) in Xcode 6 and now it's apeared again: https://github.com/lionheart/openradar-mirror/issues/8030
I'm calling someone from the Support team in this thread to find a workaround.
We had a similar problem our solution was to create a script that did the checkout of the sub-module and run that as a pre-integration trigger for the bot. Just a two liner:
git submodule init
git submodule update
One thing we also ended up doing was creating a read-only user in git that the submodule uses to checkout. You may not need that last step.
We just have bumped into the very same problem (submodules not cloned automatically) with Xcode 11.1 (11A1027).
The only work-around we eventually found was to go Terminal and use an explicit
git submodule update --init --recursive
Is it possible such a howler still was not fixed in Xcode, not even after three years? Or do we do some mistake at our side, for this should work all right and does for others? Thanks!