I think you're taking the wrong thing from it and I believe I have a quote from the Jurassic Park movie that helps:
John Hammond: When we have control—
Ellie Sattler: You never had control — that's the illusion! I was overwhelmed by the power of this place. But I made a mistake, too. I didn't have enough respect for that power, and it's out now.
The point here is that it's more about knowing what you're doing rather than condemning new technology. What was the single biggest mistake they made in the Jurassic Park novel? Hiring a guy who was untrustworthy and then paying him little. He was the one that sabotaged the park. The dinosaurs running amok are the same as opening the cage to the big predators at a zoo. If they want to eat humans, they will try.
The whole reason they destroyed the island at the end was to prevent the dinosaurs from going to other islands like they had managed to do. But they lacked control because they made more than they could keep track of and they didn't know much about the dinosaurs at all. You have to know about the creature you're holding captive to be able to keep it captive.
See, in Jurassic Park it was more of people taking short cuts than the new technology. The fencing system is pretty standard. I'll admit that he did make the dinosaurs a bit TOO aggressive at times, but that was for conflict reason. I honestly can't see how this would be cloning failing, but more or less a zoo that was poorly ran. Think about it: Hammond was more obsessed with making money than showing off his creation. Okay, I could see a greed thing about this, but that's about it.
Also, I think part of the reason they were killed was for a conclusive ending. Closure. I mean, reasoning was to prevent the dinosaurs from spreading to other islands seeing as Costa Rica was having a problem with compies attacking their young.
Let's look at Sphere:
Like I said, Sphere has nothing to do with technology malfunctioning. The Sphere worked perfectly. It did was it was built to do. The problem here was that those that got the power didn't know how to use it. Harry was the first one to get it and he didn't have control over it because no one had had that power before him. He didn't know what it could do. He didn't know he was doing anything.
Beth was emotionally and mentally unstable. She had no control there and it effected how she used her powers.
Norman, on the other hand, having observed both Beth and Harry, had known what to do. He had control over it. Truth be told, Norman is a perfect example of what I'm getting at. The technology works for him. Nothing bad happens when he gets it. He doesn't manifest a giant squid or anything of that nature. Why? He has control of both the powers and of his own emotions.
At the end, the Sphere was thought to have been destroyed because the three didn't think that humans could handle the power. I think it's the same as not going around town handing out guns and doing background checks on people who do have guns. Can you imagine a whole lot of people like Beth with that power?
In Prey:
I can't really say much about this one. I read it once back in 2004 (or whenever it was new) and haven't reread it since. But I will say this: the methods in which they made nanobots was unknown to them. They got out and ran amok because they were unaware of their capabilities. I don't recall the nanobots being taken care of in this one, either. I thought the threat was still rampant.
I still think it's the arrogance of thinking you have control and really not having it. There's no way Crichton COULD write technology in a positive light without writing essays, but he'd rather write fiction, which means he needs conflict. Rather than having this impressive technology in the background of a novel, he opts to portray it in a "negative light" so as to have conflict.
I'm going to have to pull out more examples for my point:
In Crichton's book Next, there was nothing NEGATIVE about bioengineering. In fact, I recall a happy ending with a talking parrot and an ape kid. The good guys were trying to save them both from people who wanted them for selfish reasons. If nothing else, I think Next is a perfect example of when he doesn't follow the formula.
Steve Alten wrote several books about Megalodon sharks. The sharks attack humans and large sea mammals. Does that mean he hates sharks? Probably not. In fact, I'm pretty sure he likes them. In fact, a lot of people write about what they like. I've written dragons in a negative light before, but I really like dragons. I added them because I liked dragons. I just thought it more sensible to put them in a negative light.