Missing 2 passive skill points, quest state in Act 3 well after completing campaign is unrecoverable

I've had some major issues with leveling and bugs in the campaign. I had to completely abandon a Monk I was leveling because it would corrupt the skills I inserted making them unusable (I filed a bug about this).

I am now missing 2 out of the 24 "weapon set" skill points. I have run over all the locations and bosses that award +2 weapon skill points and none of them have these points.

I have the boss Ignagduk The Witch, still un-highlighted so I went to kill that boss (a few times) and no quest items dropped or progressed; and the icon is still solid n the map.

My character seems to be stuck in this error state with no way to recover these 2 skill points.

I also had to repeat act 3 a few times because the quest state and all of my waypoints would get reset.. and that was zero fun.. so it's possible something is bugged with that.

Anyway it would be great if I can just get those 2 missing skill points fixed up.. thanks.


EDIT: I found a way to get my missing skill points. My act 3 normal has almost NO waypoints.. so I can't travel anywhere. I went to act 3 Cruel and from there I was able to see the waypoints in Act 3 again; I went back to Act 3 normal using this and found the missing points.

This is definitely a bug though.. my quest state is simply broken for act 3 normal: There are only 2 total waypoints and no bosses showing on the underground map (or overground!).

Thanks.