I must say this game is pretty bugged for me, since the very beginning, so far it is quite disappointing experience. I never had such problems with the first game..
It started right after the very start of the game, when I had to get my crew together after crashing the ship. First major bug was when I was not able to proceed to Irina (if I remember the name correctly) after climbing the Defiant wreck. When I climbed it, there was still fog of war on the deck and I was not able to click anywhere.. I had to reload a save and then fog of war disappeared and I was able to get to Irena and talk to her.
Then, in the very first town, I had the problem (and still having) with being unable to loot some chests/boxes/etc , as I already described. (btw I have a vide now, if you want it, Schin, along with a save)
Then, in Deadlight fort, I had another gamebraking bug. I rang the bell to lure the boss out into the open, cutscene started, then I talked to him, etc. Then I decided to load a save which was before talking to him, so I can kill all other pirates in the fort and get their loot (because they were friendly after talking to the boss). I did that, and returned to the bell. However, now, after ringing the bell, nothing was happening. No cutscene of ship sailing away and boss coming out.. When I checked the secred dock, the ship wasnt even there! So the game somehow remembered that I already spoke to the boss and ship sailed away, despite loading a save right before talking to him.
Another strange bug was that one group of pirates suddenly disappared , after loading a save. When I reloaded the save again, the group was suddenly there again.. (Ungwith group, to be precise). So, it seems there is a lot of bad things going on when you frequently use save/load, at least for me.
All this in first few hours of playing the game. What a disappointment.. It feels to me like my whole game is broken for me for some reason. Maybe it would be safer to start a new game from the beginning. But loosing 5 hours of my time because of bugs really sucks. Then again, I never had such strange save/load issues in any other game, and I played hundreds of them. And it seems really weird that this would be happening only to me.