Regarding Nedry, Hammond definitely screwed him.
"And partly it was insurance for the future. Nedry was annoyed with the Jurassic Park project; late in the schedule, InGen had demanded extensive modifications to the system but hadn't been willing to pay for them, arguing they should be included under the original contract. Lawsuits were threatened; letters were written to Nedry's other clients, implying that Nedry was unreliable. It was blackmail, and in the end Nedry had been forced to eat his overages on Jurassic Park and to make the changes that Hammond wanted. But later, when he was approached by Lewis Dodgson at Biosyn, Nedry was ready to listen. And able to say that he could indeed get past Jurassic Park security. He could get into any room, any system, anywhere in the park. Because he had programmed it that way. Just in case."
To my recollection, they tracked animals by height. The graph says there are Y animals of X height, from which they'd deduce 20 velociraptors at 33 and 34 cm, for instance. I think they didn't realize animals were breeding because some of the smaller ones that had escaped were in the same height as some of the broodlings. Basically, a really shitty tracking system.
The big reveal in the book of how they didn't realize there was breeding going on was the way the motion sensors counted the animals. They were set up to tally whether or not there were X number of animals, say 100. They did it this way because they wanted to know if and when any were dying. They didn't program it to alert anyone or even count if there were animals ABOVE 100. So the system would tally to 100, say "all is well, the dinos are all here" and stop counting. It didn't know or care that there were 200.
It's a great scene, when they start changing the parameter and it says "100 animals. 110 animals. 130 animals" etc
Honestly the book is so good, I need to re-read it asap