I've noticed on the new T11 format that even if you are training another position/SA to use the skill points they don't always go there and sometimes get assigned to the players %.
I buy and sell a whole team every season so I spend most of my time watching where a player is to make sure he is easy to sell near the end of the season and this has happend to me 4 or 5 times, where a player has reached 99%, he has either a SA or new position opened but still goes up to Scout, making selling him very difficult.
Annoying as it doesn't happen on the old format.