Was able to duplicate this in my user files as well as in the base d20 files. Not sure if this is cross-system or not, so I'm putting here in the d20 area.
Load a hero with no warnings that has all its skill points assigned. Add a Craft skill (or other additional skill, such as Knowledge), then remove that skill from the list. The display will now suddenly indicate that there are a lot more skill points to spend, when it is not the case.
1. Before adding a skill (d20 default Barbarian).
2. After adding Craft (alchemy).
3. After removing Craft (alchemy).
