Please chime in in the comments, if you don’t mind…
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The Dispersal of Darwin 
Two big ones:
“It’s all a random process”
“It has a direction or telos”
The most frustrating one is that natural selection is the only important process of evolution and that creationists think that if they can defeat that one, the book is closed on TOE.
The one that I have come across form resistant Christians is micro vs macro evolution. They are willing to accept variance within a species, but refuse to believe that it can eventually lead to the formation of new species.
That it is ‘only’ a theory. That it breaks the Second Law of Thermodynamics. That it proves that no gods exist. That it is linear. That it implies that chimps and humans can’t possibly coexist. That it cannot explain complex organs. That it cannot make predictions. That it is all a pack of lies.
That you can only “believe” in it if you are an atheist.
While the above are all worthy candidates, I think it may be the “Lamarckian fallacy” (that entire groups/species have to morph together upwards on a scale of complexity), which is the basis of that most basic characteristic of creationist arguments: “If we evolved from monkeys …”
This “all or nothing” thinking is also the root cause of such inanities as Ray Comfort’s thinking that males and females have to separately evolve and ask how males and females just “happened” to evolve at the same time.
It’s even the source of the IDer’s “irreducible complexity,” since to get, say, the bacterial flagellum, there had to be coordinated steps from what was to what is in a direct line of assent up the “ladder of creation.”
“You can’t just grow information [DNA] from nothing!”
Well, sorry to disappoint..
Evolution moves towards ‘perfection’
Humans/Plants don’t evolve
Confusing Natural Selection and Evolution
Previous posters have hit the biggies, but i cast my vote for teleology as the #1 misconception about evolution.
Here are the ones I most often encounter:
1. It’s “only a theory”.
2. It can’t explain how life arose (which creationists never understand it’s not supposed to).
3. Only changes within species have been seen, not from one species to another.
4. Evolution implies immorality (at the extremes this becomes “Evolution begets eugenics.”)
5. There wasn’t enough time for the mutations to have occurred.
6. We don’t have the “missing link” fossils.
7. Evolution is random.
8. There is no way you can increase genetic information.
9. Evolution is like saying a hurricane through a junkyard can make a jumbo jet (Hoyle’s fallacy).
10. (Believe it or not this one I’ve heard from atheist westerners and Muslim arabs): Evolution was invented on purpose to undermine humanity’s belief in God.
Many more – including the 2nd Law one mentioned in other comments – but I’ll leave it here.
Thanks, all! I am writing up a 10 Myths & Misconceptions about evolution handout for CFI Portland’s Darwin Day this coming February.
That everything produced by evolution has a function (i.e., purpose) when in fact many initial characteristics evolved in a strictly structural sense.