So the bugs I faced
-Taking Brotherhood Leanings didn't lock an End to Privilege or The Empire
-Establish Official Communication doesn't do anything
-Chosen one doesn't do anything
-the Whole Naval tree with research bonus is not worth going into due to naval research already being extremely low
-I can do the focus that effect a nation you're supposed to Annex before annexation

When the NCR civil war starts and the Brotherhood declares war on the Enclave, the Brotherhood takes back all of the bay area that you get from the focuses.

The biggest bug I have is at some point my army all of sudden gets no supply and they cant do anything. This happens and I have no idea why I have high infrastructure but when I go into supply mode it doesnt even show my army taking supply at all and they just die.

For some reason when I play this with the Yakuza mod on this tree replaces the Yakuza's tree as well, dunno if this is an issue with your mod or theirs.