Lots of folk have noticed this by now but years ago when I first got it on dvd, I paused the part in Alien 3 when Ripey thinks she sees the Runner which turns out to be a pipe, however by pausing it, you can clearly see that the Alien was actually there, so either she was hallucinating or the thing moved really fast before she could strike it.
Before I wasn't sure due to the area resembling the biomechanics of the alien, also during that scene, the basement looks similar to hive, just its metal pipes, wires and wierd walls instead resin.