Skill tree ponits lost (Bug?)

To summarize my problem: I rebuilt my skill tree, played a bit more. So far everything is fine.
Defeated monkey boss (act 6), used the “book” for the 3 extra points. Opened the skill tree to distribute the points. Realized that my skill tree looks in parts as if I had never rebuilt it.
The gold for reskilling was gone.
And I'm missing 2 of my skill points.
Restarting the game or checking the game files didn't help.

Bug ID: #691843096