Think of it like this. You've got a dog. Your dog is very smart. She knows her name, she does tricks, she has a pretty apparent understanding several spoken words, tonal inflections, and body language, and can even catch a frisbee out of the air when you throw one. However, no matter what you do, no matter how hard you or she tries, your dog will never understand calculus. A dog is simply not capable of understanding what calculus is or what it is for or how it describes relationships of objects in Newtonian physics. There is a fundamental physiological limit to her intelligence, and topics like calculus are beyond it.
Humans are much more capable than dogs. However, humans are still physical beings. As such, they have physical limits to brain size, and physical limits to brain activity. We also have a limited life span, so if something exists which might be comprehensible to a 200 year old human, we may never know it. It is most probable that there are concepts, topics, and systems that are simply too complex for human intelligence to understand even if we had access to the equivalent of a Calculus For Dummies.
Worse, human brains are limited to their senses, and scientific understanding is contingent on both observation and repetition. A system can only operate on the data it has available to it. If something exists which either cannot be perceived or cannot be repeated, then we have essentially no capability of even knowing that we don't understand it. The fact that some of the most complex systems have been understood though abstraction, encapsulation, and modeling doesn't mean that all possible systems will behave that way or can be understood that way or, frankly, even that the knowledge we gain about systems that way can truly be called "understanding." How often do we say, "It wasn't until I experienced it myself that I understood"?
As far as AI, well, we don't even know if they're capable of consciousness or sentience, let alone sapience. They may just be arbitrarily complex systems good enough to simulate human behavior and fool a Turing test. No, passing a Turing test doesn't mean you're conscious or sentient; it means you're not definitely non-sentient or inanimate. And if the basis of everything an AI knows is what they learned from us using algorithms we decided to give them, what does that mean they won't be capable of just because we're the ones that taught them?
TLDR: The universe is not obligated to function in a manner comprehensible to human intelligence.