I have encountered this bug a couple of times, but rarely, when I try to level up an officer, the two skills I usually have to pick from are absent. It usually only happens to one officer at a time, but when it occurs, it stops all future leveling of the officer as no additional skills can be chosen, and the skill tree picks for that officer appear to be saved.
Perhaps you could have an officer with a pending level up have their available skills reset upon loading a save, or restarting the game. That would prevent an officer from becoming permanently locked in this state.
Here is an image of an officer with a blank skill window:
https://drive.google.com/file/d/1MY5JI5KlNP7N806_4NPaPUDwLKC0cNEJ/view?usp=sharing