These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Special Effect Failure: The aliens prosthetics in Species III are vastly inferior to what was seen in the two previous films. The Awakening has similarly bad effects, but for the most part it does a better job of working around them.
In the first film, the "mist" in the woods outside the hot tub guy's house is patchy, obviously from a smoke machine. Also the Conspicuous CGI in the final scenes (which H.R. Giger complained about, saying that unlike the animatronics they weren't worthy translations of his design).
Strawman Has a Point: In the first film, Xavier says they made her female assuming she'd be more docile - but they actually may have bought themselves more time, considering in the sequel we see first hand the damage an attractive male can do when he can have multiple partners at once.
Unfortunate Implications: in Species II when Marg Helgenberger's character says that Eve shouldn't be held responsible for her actions and is human too, one of the other characters rebuts her by pointing to the cocoons of the infected astronaut's metamorphosizing offspring and saying "like them". Keep in mind, as far as we know the infected astronaut's children haven't actually done anything bad yet (well, aside from killing their mothers, but that's like holding a human responsible if his mother died in childbirth). Our heroes are about to slaughter them in their sleep purely because of what species they belong to. I'm not saying this isn't justifiable under the circumstances, but if you can have sympathy for Eve you can have sympathy for them. But when they're up there in those cocoons they look obviously inhuman, and that means it's obviously OK to kill them. In the movie they all seem to be portrayed as male, so one suspects a degree of The Unfair Sex is involved as well.