If you have a drain effect spell active, you can train at a lower cost. But if you train to 100 while the effect is still active, when the effect is removed, the skill will recover what you lost. I don't think having any skill over 100 has any real benefit though. Maybe a few.
Yeh the problem I think is that my level was actually about 81 when I used a dupe glitch to get it up to 91. So I trained with the master trainer to get to 100, but the master level pop up didn't hit, so I think what I have to do, since I'm level 106, is play like I'm actually 96, and train 4 more levels to get that pop up. Because even though it says I'm 106, it still refers to my skill as expert.