It has been happening occasionally, but I wasn't 100% sure before. My 2 henchmen leveled, and I learned my next spell for my lvl 12 Primabolt (FA regen). I checked my plat total, then clicked the timer on the spell being learned (showed 7 plat to insta-learn). My plat total lowered by 7, and the spell displayed as learned. I unchecked essence of wolf spell so I could memorize the new one. When I went to check the new spell to memorize, nothing happened. I refreshed the game, and it showed the spell was still being learned, and needed another 7 plat to insta-learn. The first 7 plat spent was still spent according to my total plat. I clicked it to do so. Again, it displayed as learned, but now I could click it to memorize it.
No idea , how many times this has happened to me, but I am thinking quite a few on spells since the timers have grown over a few minutes. I can't confirm if it has happened on skills.