I think one of the big reasons is in comparison with the first two movies, which really end on upbeat notes.
Alien for example, as dark and intense as it is, has the most peaceful and relaxing conclusion you could ask for in a movie about space rape, further enhanced by Goldsmith's score. This was later repeated in Aliens.
What these two films did so successfully was put the audience on a ride which offered no guarantee of safety or a happy ending, but still gave it to them in a way that didn't feel like a cheat. With the bittersweet nature of Alien 3s conclusion, it is understandable that some would feel blindsided by the tonal shift.
It is by no means a bad film, but it does have a lot of issues, and Hicks n Newt are the least of its problems.