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There are several "issues" in Jurassic Park. By issues I assume you mean conflicts, which are a form of literary plot device that depict a contradiction between the ideas or objectives of two or more elements.
I would consider there to be three levels of conflict in the story. The first are conflicts of ideology, which have to do with morals, philosophy and other means of interpreting the "big" questions. The second are large conflicts directly relevant to the narrative, and tend to span several chapters, such as the power going out, the animals getting loose, or a character like Nedry attempting to keep his actions secret. Third, there are lesser aspects of the narrative conflicts, usually derivatives of the larger ones, such as the animals adapting and breeding.
I think the most significant conflict in the story is a "Frankenstein" message, but one with more positive overtones. In the original Frankenstein, the message was clearly that the gift of life did not belong to humans, and though Victor Frankenstein succeeded in giving the Monster life, the Monster found no joy in it, and Frankenstein was destroyed by his own hubris. In contrast, the message from Jurassic Park is that, while man may play the part of Frankenstein and think he has attained godhood by resurrecting an extinct species, life instead takes control away from man and, like in Frankenstein, "punishes" him for it. The animals do not despair because they have no humanity to reflect upon; by acting as agents of life itself (recall the line "life will find a way") they have no remorse for their dead ancestors or their monstrous appearance in the modern world. For this conflict, the central theme is the illusion of control, not necessarily the morality of control.
In a broader sense, I think the book also depicts a "man vs. himself" conflict, in that many of the characters who could and should have questioned the sanity of the project failed to do so, simply seeing themselves as passionate researchers and small parts of a collaborative whole, but unfortunately for them, dinosaurs don't care whether you're morally responsible or not; they just eat you.
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