Not getting far into the campaign is an issue I have myself.
I always start from the beginning, and end up quitting because of a bug before I even get radar. The CO2 bug I wasnt even aware of before I got UBM (which I just got, which in turn I guess is why I'm ranting) It places a nice warning onscreen. I wonder how many of my fleet boats have previously been mysteriously lost at sea, when all they had to do was open the hatch.
The graphical glitches are numerous, but the worst ones look like big round smoke "bubbles" that appear close'ish to the ship on top of the water when I have spotted a ship far far away. Also the lack of funnel smoke. Compared to the background menu movie, I have no smoke coming from the funnels. I have however smoke from fires and explosions. The screen also flickers sometimes (I have a Nvidia 9800 GT which should run it ok) and the conning tower helmsmen are transparent in a scary way, though not as scare as when they loose their eyes. The nightsky looks almost like Northern Lights sometimes (I think its a fog/moonshine godrays issue) and the raindrops just looks silly. the raindrops I fixed with websters smaller raindrops.
The savegame issues appear out of nowhere, but it might be helpfull to save without ships around and surfaced, though its usually in close encounters a save is needed. I have made a habit of keeping 5-10 savegames, named after location/action such as Cruising/Hunting/Convoy/Attacking/Harbor/Office etc etc, but sometimes a hunt and kill can take hours (I play 100% realism except event cam) and reloading can be a mood killer...
The office crew problem was related to changing subs and the deck crew. I cant remember exactly what happened, but I think they got bugged, so the deckgun couldnt be used if changed to Bow position. It looks like they might have fixed it in UBM, though I havent tested yet.
These are the issues that I can think about on the top of my head, but many more lurks in the deep waters.....