As Minmay said, there is nothing you can do to avoid this bug, it will occur whatever you do when the player learns a new spell. So the only thing you can do is tell players to not use the import function (a shame for an official feature!), or point them to my tool to clean save game files.
PS: I am a little tired of this one, you wouldn't believe how many times I see this everywhere in mod discussions!
A script that work for one player but not for another one...
Re: A script that works for one player but not for another o
You're right AndakRainor, I should edit the description of my mod to prevent this kind of bug. And with your permission, I'll point to your Save Editor 
Khollik
Khollik