It's kind of like the "monad tutorial" problem in software. Everyone tries to reach for analogy for that computational structure. Although there are some decent ones, in the end, people who work with monads just have to accept the monad laws (sort of a parallel to the data that physics has on quantuum phenomena) and eventually they develop a sense of what they are independent of cafeteria trays and burritos ( http://codetojoy.blogspot.com/2009/03/monads-are-burritos.ht... )
As a CS graguate, I would call it the halting problem. A mathematician would refer to the Gödel's incompleteness theorems. No formal system without paradoxies can be used to prove all true statements.
In other words, as michaelfeathers said, "the map is not the territory."
I'm surprised this way of seeing the world isn't more wide spread. My opinion is that it should be among people who have a deep interest in science.
Perhaps, the biggest philosophical problem with waves are their integration requirements and the potential for such iterations to exceed cosmic speed limits. When the function is continuous a perturbation at one end must effect the other end.
I don't know much about physics, but my take on this is:
First you model reality with waves and particles, then you see that particles can behave like waves and vice versa. The next step is to model reality with something different that can behave like a wave AND a particle and suddendly there is no paradoxon anymore.
As a teen I read a book by Robert Anton Wilson that made an interesting point. We have experiments showing wave-like and particular-like behavior but all we have is that data and we can accept it at face value without having to impose the idea of a wave or a particle on it. "Waves" and "particles" are, like you say, analogies.
There's no particular reason the phenomena can't behave like both, and, in fact, they do. It's only a paradox if we choose to analogize. We don't have to.
As Korzybski said "the map is not the territory." Trying to resolve wave/particle duality is trying to impose one of two maps from other territories to a new one.