Philosophy categorizes several different types of arguments: one argument type is of logical necessity, arguing from experience is another, as is arguing from authority. Most arguments are pretty easy to identify. "This person is an expert in the field and she says X, so X must be true" is an argument from authority. The expert may have a different argument: "Under these circumstances, I've seen X and only X happen," which is an argument from experience. Unfortunately, there is another type of argument that people like to use, an argument from ignorance.
I'll start with a non-religious example. In a magazine article that shall remain nameless, an expert in materials engineering who also happened to be an Egypt buff wrote about his research into obelisk carving. He found a written record stating that a particular obelisk was being carved for a period of time but then the obelisk cracked and the project was abandoned. He then located this abandoned obelisk and noted how much of it had already been carved. Using his considerable skills in materials engineering and after conducting field-tests on rate-of-removal speeds with the tools ancient Egyptians were known to use, he determined that there was no way they could have removed the amount of rock they did in the available time. It was impossible. Thus, he concludes, aliens must have helped the Egyptians.
On the surface, this appears to be an argument from authority, but it is really an argument from ignorance. One other little story may help show this. A person I know grew up in a family that worked with rock. He was learning how to build rock walls, and the like, from his father, who learned from his father, and so on for generations. On the job-site, he watched as workers pounded away on rocks for hours, trying to get them into the right shape for the job at hand, while his father would pick up a rock, look at it, whack it once or twice, and the rock would split apart leaving the necessary shape behind. Because of this skill, his father could do the work of several other men on the job. There are many, many books on geology and working with stone, but the skills his father had to understand rock and work with its internal fault-lines is not something that's in a book. Even if it were written down, it's not something a person could learn by reading. It takes years and years of experience.
So, back to the Egypt example, we have an expert faced with two possibilities: 1) Ancient Egyptian craftsmen, being at the hight of stone-age culture that spanned all the way back to Homo-Habilis, might have known something about working with rock that he doesn't. Or, 2) Aliens came to earth, made contact with the ancient Egyptians, and instead of helping them with medicine, mathematics, or even weapons, they helped them carve big chunks of rock, which they screwed-up while doing such that the obelisk cracked and they had to start over. Given these two options, our expert chose the latter.
This is a typical argument from ignorance. X is impossible, so - insert favourite theory here - must be true; the Egyptians couldn't remove that much stone in the given time, so aliens must have helped. Not only is this type of argument incredibly arrogant, in stating categorically that something is impossible just because we don't know how, it is also incredibly weak as far as arguments go. Anyone wanting to counter this argument merely has to, in an argument from experience, list off the thousands of examples where ignorant people had concluded that gods were doing something, only to be proven wrong by science. There are flashes of lights and booming sounds coming from the sky; I don't know how that happens so the gods must be angry. I don't know why the sun disappeared in the middle of the day, so the gods must be giving us an omen. I don't know why it rains, so the gods must make it rain. The list is very, very long. Experience shows that while we may not know how something happens, it is a bad bet to assume that gods or aliens did it. It is far better to just say: we don't know how X happens, yet, but we'll probably figure it out at some point down the road.
Science often makes mistakes but it is also a self-correcting endeavor. When faced with one of these arguments from ignorance, a scientist will attempt to come up with alternative solutions. Things don't fall down because a god pulls them down, they fall down because of a predictable force called gravity. When one of these hypothesis gains widespread approval, it becomes a theory and, being the most likely solution, is the one taught to new students of science and used for explaining things to non-scientists. However, if enough proof comes along that the theory is incorrect, or incomplete, then it can change. The original theory of gravity has been somewhat replaced or augmented with the theory of relativity, which is being augmented even today. The theory of relativity also happens to be one of the most tested theories in all of science. Yet, someday, it too may be replaced with something better. As such, there are always competing hypothesis that are trying to replace accepted theories. That's how science works.
The evolution of species is a widely-accepted theory. It is what is taught in science class and is what is used to explain things to non-scientists. Life is a very complicated thing and this theory is not a complete explanation; there are things that remain unknown. Further, there are many competing hypothesis covering a myriad different aspects of the overall theory. Some scientists maintain RNA based origins to life while others suggest a more simple chemical synthesis route, for example. However, this ignorance does not mean that God did it; dissent within the scientific community does not mean that we know nothing.
People make arguments along the lines of: X is the mainstream scientific theory to explain Y. Scientists have shown an element of X to be impossible. Thus, X is impossible, so God did Y. By now, you should be able to recognise this as a classic argument from ignorance. While an element of X may bring its validity into question and leave us in a more ignorant position on Y, that just means that we simply don't know everything yet. Experience shows us that arguments from ignorance are useless; just because we don't know how something happens, it does not follow that gods of aliens did it. It just proves that we don't know everything yet.