I tried putting Mateo Nuñez into psi training. He had 0 skill before, 0 skill after the month changed, and 9/+9 skill after a month. You should get 6-9 for your first month, so that checks out. So I don't think getting negative skill from training assignment is the problem.
Do you have any saves immediately after hiring these negative-psi-skill agents?
Edit: The game not showing or using negative skill is true.
Mateo Nuñez also has been in the gym and continued during that month, so I don't think regular training is the culprit, either. And some of the problem children are absolute rookies, so they couldn't have been hit with some psi-draining effect, either.
Puzzling.
Edit2: You can try hiring new rookies and checking whether they're okay in the save.