We have detected one event of keystone not adding users to the bastion project after such user being added to other project.
Update: I double-checked both the keystone code and cookbooks involved in the process and they work correctly when I'm watching. We now have monitoring for this issue, and I wrote a runbook explaining causes and solutions here:
https://wikitech.wikimedia.org/wiki/Portal:Cloud_VPS/Admin/Users_not_in_bastion_project
Now we need to wait to see if/when this happens again and investigate.