The setting and plot make basically no sense, it was badly-written and had incoherent editing, and was only really a "movie" in the strictest sense after they edited the plot back in with the Quadrilogy/Anthology release.
My problems with Alien 3 are the producers. They had a script by William Gibson, which they eventually scrapped, so they could write their own script that fused two completely and incompatibly different scripts about a monastery planet and a prison planet. They had David Fincher, one of the most celebrated directors, whose work they chopped up because they wanted to assemble their own film from the scraps. Problems, thy names are David Giler and Walter Hill. They also went on to do the same thing to Alien 4, AvP, and AvP:R.
Fincher is the only director who refused to do a re-edit for the Quadrilogy because he didn't want to work with Giler and Hill again. Fincher is also the only person whose audio commentary was edited out of the Quadrilogy, because it was critical of Giler and Hill. Incompetent? Ego-driven? Responsible for filming more disasters than Dean Devlin and Roland Emmerich? You betcha.