What possible happened is the State Dept weenies decided that it was too much work and inconvenience to deal with the systems that manage top-secret documents, and so classified lots of stuff at a much lower level than they should have.
That is what I think happened.
God forbid the incompetent, lazy people at the State Department actually get off their butts and do WORK.
The State Department has been staffed with liberals (and communist sympathizers/members) since FDR took over, and probably before that.