It's been mentioned in a few places now, but Larian's idea for this EA release was to 'encourage' people to play in a more evil role, so they could gather more data on this aspect as more people tend to go for good options all the time. So the situations you mention are pretty much railroading you into the evil option, ie. killing Nettie to get the antidote (btw I have also experienced this bug, where she talks to you as if you are poisoned even if you persuaded her not to previously).
As others have mentioned, the idea is that the game will (eventually) have enough depth so that 'winning' every conversation check is not required in order to make satisfactory progress - by save-scumming checks you are potentially missing out on 'alternative' content from the failed check, which may have repercussions later on in the story.
The situation with the imps and the helm objective, well that requires a little 'outside of the box' thinking on the part of the player. Same with the illithid and fisherfolk - when they become hostile that doesn't mean you have to attack them, you can target the illithid with your first attack which will release them from it's control. As a DM of 35 years I'm a little surprised that this not only didn't occur to you, but you think it is a fault of the game. And a level 1 player attempting to battle wits with a mind flayer... how do you really think this action should play out?
I and many others agree that there needs to be a system for rewarding non-combat XP, perhaps this is something they have in the pipeline. Also some of the other issues like spell movement are clearly bugs that need to be rectified. Again, EA.
In summary though, I think there are reasons for most of your issues which hopefully now make a bit more sense to you.
But it is the game's fault, because Larian expects you to know everything about the DoS system, the D&D system in the latest edition and have a really good grasp of gameplay tactics and an inquisitive mind with good intuition, as well as an awful amount of luck. That is way too much to ask for.
Your example is great. I did not even know I could attack the Illithid, because I did not even see it under the debris, and he never lit up. Oh the loading screen tells me that I can attack environment objects and neutral people with STRG, but they do not tell me how I see all of the possible interactions. For me the only visible options were persuasion and attacking.
Nettie is another great example of the game not giving you crucial information. Again you are presented with attacking and persuasion. However there are at least 5 ways to deal with the situation, including pickpocketing, something never explained to me so far. There apparently is also a cauldron to brew up your own potion. But again, it does not light up, so is it just fluff like chairs and benches, a container like the thousand empty bookshelves, something I can interact with in combat, or an actual tool for bringing forth the story? I never noticed it. My solution was to look for a secret backdoor that led me to a cave, where I could not progress. At that stage I was so invested with this possibility than naturally the others did not occur to me at all. So I reloaded until I passe all three checks, because I could somehow anticipate the outcome.
In combat it is even worse, because it varies between ridiculously easy and incredibly hard depending on your knowledge and willingness to exploit mechanics.
