I am sorry as I don't have screenshots and logs and such. Hopefully descriptions suffice.

I am running with all DLCs on Win10 professional 64 bit.

1. Naval quest "Scripts and Scrapes" calls for a strong hero (lvl4) to visit a sunken ruin. I tried with 2 different heroes (Morgawr and Haunts) at level 4 and 6. It still considers conditions unmet.

2. Quest to get x luxury facilities to pacify a fortress would complete if I get the last luxury by capturing the fortress that gave the quest, but red error screen shows up.

3. Another fortress pacification quest to visit a ruin remains active even if i capture the fortress by force, and then when I visit the ruin and complete it red error shows up. 

In both cases 2 and 3 I can hit "continue" on the error message and it's ok. 

The last one not really a bug but maybe a balancing issue.

It is really a late game thing when you dominate already and as such impact may not be too important. 

Still you can build ships for 0 production, so you basically can produce 100000000 ships in one turn. 

You need naval architecture facility, 20 owned fortresses, military plan lvl1 and morgawr hero with 2 points in shipbuilding skill.

Perhaps, naval architecture facility should be toned down to 1% per fortress instead of 2.