It seems that you're making an assumption that God programmed it in. It's altogether possible that such behavior evolved as part of the "survival of the fittest" phenomena that perpetuate life. Possibly it's not programmed in at all. I'm guessing you have no basis to assume or presuppose "God is the programmer of animals and nature". But then you instantly jump to the conclusion of a malevolent God. Why is that?

I'll say this: God as the programmer of all nature isn't a biblical teaching. Evolution is possible in the biblical model. And you shouldn't be so quick to deprecate God based on possibly false premises.

Why would a benevolent god program this behavior in primates (including humans)

So I was watching videos on gorillas and their mating practices. Apparently the alpha male gorilla mates with most of the female gorillas, but there are some low ranking female gorillas that he refuses to mate with. These low ranking female gorillas will try multiple times to mate with this alpha male gorilla and he rejects their offer every time. So the female gorilla gets so desperate she goes towards a low ranking male to mate with, and of course he accepts. Then all of a sudden the alpha male gorilla comes charging out of no where, even though the low ranking gorillas were out of his sight, and he basically scares off and intimidates the low ranking male gorilla so he can't even mate with a low ranking female.

This reminds me of similar behavior in humans. I remember in high school if an ugly low ranking male got a girlfriend, even if she was ugly and was unpopular, the top males (usually jocks) would come up to him and bully him in front of her so he basically gives up and she loses her sexual attraction to him or just gives up out of intimidation or fear. Also this doesn't happen just once, I remember the bullies would really work at it and use continued harassment.

This honestly makes me doubt a benevolent God. Why would he program such behavior into the gorillas like that? Why can't all male gorillas pair off and be monogamous, why is there always one male controlling it all? God is the programmer of animals and nature so he could simply make most mammal species monogamous.