Question

Hello Rabbi, and happy holiday!
I wanted to ask you a question that has been bothering me for quite some time. Just for clarification, I belong to the Religious Zionist camp, and I have no intention of raising difficulties just for the sake of it. I simply came across a question that occurred to me and gives me no peace of mind, and I have been trying to provide myself with an answer without any success, so I turned to you in the hope of finding a response.
So here it is: I searched quite a bit, I think, and did not find in Judaism a rational answer to non-harmonious phenomena in reality. Just to be safe, since I do not know whether “lack of harmony” is the precise term to describe the phenomena in reality that I mean, I will give a few examples.
Not long ago, at home in the fruit basket, I found two bananas sharing the same peel, something apparently unusual in the natural order. Another example: not long ago I read online about a brown-and-white panda bear, and that it is the only one in the world. These phenomena and others like them appear, seemingly, as unusual occurrences in the natural order of the world, something that could indicate a lack of intelligent design.
Another type, somewhat different in definition, of non-harmonious appearances in reality—I suppose they can be called that—is things that do not deviate from the natural order, yet in some sense seem unplanned, like random side effects that are hard to attribute to the product of an intelligent designer.
Again, I will give a few examples: connected eyebrows, bodily secretions, itching on the body, beauty marks. Maybe at first these examples raise a slight chuckle, but after some thought it is hard to attribute all these phenomena to parts of an intelligently designed system. These phenomena, again apparently, testify to a lack of planning or intelligent intervention in reality, since it is hard to ascribe to them an intelligent image.
And just for clarification, I do not expect Judaism to provide an answer for every specific “non-harmonious” case in reality. I do not expect to receive a spiritual explanation for why two bananas share one peel, or why sometimes there is itching on the body. But I do expect to receive a general rational answer to the phenomenon of “lack of harmony” in reality. What role does this serve in our world?
If I compare this to the phenomenon of evil in the world, for example, then I do not expect to receive a specific answer to why the Holocaust happened (and there is no such answer, nor should there be), but on the other hand I do receive in Judaism a rational and comprehensive explanation for the role/meaning of evil in our world in general (a little visible good, hidden good, atonement for sins, etc.).
I would be glad to know and hear from the Rabbi whether there is a rational theistic explanation for the phenomenon of lack of harmony in our world—preferably from a Jewish source, if there is one.