I had this happen to my teen spellcaster. She levelled up from apprentice to neophyte by experimenting with a cauldron but didn't get the 2 perk points she should have gotten. She is now a neophyte with 0 perk points.
Also noticed the perk bar was acting weird during experimenting, going very fast up and down when starting or ending the experiment action.
I have the save where she is bugged but I use mods with this save so I don't know if it's worth sending to EA even if I would remove my mods and she would stay bugged? I tried a back up save (from main menu) still with my mods on but couldn't reproduce it. This time when she levelled up she got the points as supposed.