So that eyeball creature left the facility, went in the jungle then on the beach revived the Dr who's chest was busted. Yea... Na.
How is it boy genius didn't have a fail safe for these droids if they went rogue? Again Wendy making the xenos into pets which is silly. And how did the Xeno hear Wendy from the jungle.
It ended really silly.
Boy genius was warned that Wendy was able to hack into systems (including security cameras) but didn't think it was a threat, because he was the genius (forgetting that a human intelligence in an artificial set of hardware is likely to process stuff much faster), and it was shown on screen that at least some of the safeguards (the monitoring of their location and status) could be easily turned off via a simple management interface with it potentially not being possible to turn it back on remotely (you've closed the link down, in the same way it's entirely possible to shut down a connection to a remote computer now, and have to have someone go over and turn that link back on).
She didn't turn them into pets, she was communicating to them in a way that the either saw as a command from a more senior xenomorph type (queen, royal guard, warrior) or that they were willing to go along with because it works for them, a good portion of the better extended Aliens universe books explore that to some degree as the xenomorphs are smart enough to understand risks and play for time. Even Aliens had Ripley who was not able to "communicate" to get the warriors/drones to understand a threat to the eggs/hive and stay back waiting for a chance, and the queen very much understood it.
The noises the aliens use are explained in both the TV series (and books etc) to often be outside normal human hearing rage, Wendy was being shown very early on to be able to hear them (and IIRC the scene where they were testing her hearing showed she was capable of hearing well outside human range), and there are frequencies of sound that travel very well even in the human hearing range (one of the reasons we use things like whistles for emergencies and sports is the sound carries very well), yodelling and similar human forms of communication were developed specifically to allow simple messages to carry for miles, now think of how "loud" you could "whistle" and it not really be noticed by people if it's well outside the range our ears can pick up? especially a range that's not in use by the main local fauna

Remember you don't need to be able to send very complicated messages over long distances, a very simple call can carry a lot of information just in the tone/repetition, as someone once put it, a scream doesn't actually have much information in it and varies a lot, but it gets your attention and tells you something (probably bad) is going on and an idea of where it is