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The problem is that this is completely different from how evolution actually works. Evolution is the accumulation of very small changes over a large amount of time. You don't have a regular human have a random mutation that makes their kid have powerful beams shooting out of their eyes. Those big jumps just don't happen. Of course this is further confused by somewhat controversial idea of punctuated equilibrium where large jumps in evolution happen in a short period of time. Of course, this is on an evolutionary time scale, in the range of 50,000 to 100,000 years. This is a far cry from a normal human having a child who has the ability to walk through walls.
Unfortunately, many people never learn what evolution really is. This type of thing is their only real exposure, is it really a wonder that they think evolution is ridiculous? Is it a wonder that we get questions like "who did the first wolf mate with?" They expect that there are these huge jumps, what are the odds that an incredibly rare jump will happen to two individuals at the same time so that they can mate and carry on this new species? "The odds are astronomically low!" Of course the odds are low for what you are describing, and that's not even close to how it works, so don't worry about it.
Of course X-men isn't completely at fault for these kinds of misconceptions, the real problem is the giant gap in our education system and the people actively spreading disinformation. But it seems to me that X-men plays a role, it gives people who haven't been presented with the real information an excuse to dismiss it out of hand. I was in that group when I was in high school, I never learned even the absolute basics of how evolution works and was told in church that it was nonsense.
Now don't get me wrong, I love the X-men, and I often enjoy other shows that are basically just X-men by another name (this post was actually inspired by The Tomorrow People). But it irks me when they explain the powers as evolution, because it is not evolution at all. I wish they would make up an explanation that involves things that don't exist, a science experiment that went wrong, a flying saucer that somehow gave random people these powers, or hell, just say it's mysterious where these powers are coming from.