For a while I have had this when setting up a project on Linux: ERROR: Toolkit metadata file './info.yml' missing. Core is not fully deployed after this, and shotgun_api3 not at all.
Then I need to manually run ./tank localize and the project seems to work fine.
I have run into this from time to time when deploying our distributed config with bundles from github. Unfortunately I don’t recall if I ever found the root cause but I think I brute forced things by deleting the cache and then re-loading the config which fixed it.
The root cause would be nice to figure out though.