Bugs:
The decision to trigger a civil war in the NCR stays grayed out even after completion of the relevant focuses
There is a similar problem with the Legion slave revolts not triggering
If you puppet raiders or tribals, the focus that gives you war goals on all raiders or tribals does not give you goals on them. This is a problem because they can get to the highest level of autonomy but not become free, making it impossible to get them unified.
There is no clear explanation of which tribal and raider nations you can take the decisions to attack
Annexing NV after puppeting it will lock you out of the relevant branch of the focus tree.