Well sure, every movie has loads of flaws and internal inconsistencies, but I'm talking about deal-breakers, especially with the series plot itself.
Alien life cycle is a constant nerf, just all over the place thanks to AvP. I suppose I'll find the bulk of glaring canon offenses from AvP onwards, and the EU is going to be a chore with things like the Earth War, Queen Mother, Yautja, etc... I mean I definitely won't ignore things from Alien3 and Resurrection, but even those movies had errors within the normal level of movie gaffs. They seemed almost unintentional, and poor Alien 3 had such a hell of a time in production, I think we should be glad with the movie we got.
Plus a lot of Res is explained away by genetic tampering. Kind of nice, if you think about it, just a freak one-time occurrence.