It’s pretty hard to find too many professional philosophers who mock the traditional arguments for the existence of God even when they disagree with them. I would suggest part of the reason for this is because they, very often, know there are various forms of these arguments and they are aware of responses theists have offered to possible criticisms. Having said that there are some atheist philosophers who have not done sufficient homework in philosophy of religion and yet attempt to interact with the arguments while getting them wrong.
What I intend to compile here are a few misrepresentations of arguments for the existence of God that exist in modern atheistic literature. Since many atheists themselves now consider Dawkins and other New Atheists to be an easy target (and admit they get the arguments wrong quite openly) I will therefore restrict myself to professional philosophers who are atheists since most of them tend to avoid New Atheism. Having said that I am going to begin with the one glaring anomaly to that generalization.
(I’m going to keep adding examples as I find them so if you know of any not documented here please let me know and, if I agree it’s a misrepresentation, I will add it.)
1. Daniel Dennett‘s Breaking the Spell:
Dennett only manages six pages on arguments for the existence of God in a book which is over four-hundred pages long in total. Brevity is okay if you can manage to explain complex arguments succinctly. Unfortunately Dennett cannot when it comes to philosophy of religion.
On the cosmological argument he says:
“The Cosmological Argument, which in its simplest form states that since everything must have a cause the universe must have a cause – namely, God – doesn’t stay simple for long.”
Students doing philosophy of religion at A-level standard (pre-undergraduate degree standard in the UK) might be excused for such a poor rendering of the argument but, even then, they’re not going to score too highly either! Of course, if any theist had argued that “everything” must have a cause they would be arguing against the existence of God! Fortunately for theism and unfortunately for Dennett, theists have not used this argument.
Notice this interesting caveat at the end of his, less than half a page, critique:
“Unless you have a taste for mathematics and theoretical physics on the one hand, or the niceties of scholastic logic on the other, you are not apt to find any of this compelling, or even fathomable.”
Daniel Dennett Breaking the Spell p.242 
I don’t understand it therefore it’s wrong! Well, it almost sounds like it.
Dennett avoids directly misrepresenting the ontological argument but his treatment goes no further than pointing to Gaunilo’s objection (although modified from an island to an ice-cream sundae) but, of course, he does not mention any of the many responses made to Gaunilo’s objection. The most famous modern philosopher who has contended for the veracity of the ontological argument (Alvin Plantinga) is, not surprisingly, completely ignored. 
Le Poidevin begins his discussion on the cosmological argument like this:
“In this chapter we shall look at three versions of the cosmological argument. The first I shall call the basic cosmological argument, because the other two are modifications of it. It goes as follows:
The basic cosmological argument
1. Anything that exists has a cause of its existence.
2. Nothing can be the cause of its own existence.
3. The universe exists.
Therefore: The universe has a cause of its existence which lies outside the universe.”
Le Poidevin then immediately admits this:
“Although no-one has defended a cosmological argument of precisely this form, it provides a useful stepping-stone to the other, more sophisticated, versions.”
Le Poidevin Arguing for Atheism p.4
Although Le Poidevin goes on to discuss, what he calls, the temporal cosmological argument (similar to the Kalam but not quite the same) and the modal cosmological argument it’s most curious he begins with a form of the argument which, as he admits, no theist has ever defended. It’s also very disappointing that he does not explore the most discussed form of the argument in modern times (the Kalam) and yet he gives a page of discussion to a form of the argument no theist has ever defended. Odd to say the least.
Even though Massimo Pigliucci considers the British Humanist philosopher Anthony Grayling to be outside of the New Atheist movement, it certainly appears he shares their zeal for getting theistic arguments horribly wrong. Grayling is a top level philosopher who sits on the editorial boards for numerous philosophical journals and who has lectured in philosophy for many years.
Having said that, listen to him introduce the moral argument (or course – those of you well read in philosophy of religion know there are many versions of this argument):
“What of the moral argument for the existence of a deity? Stated at its simplest, it is that there can be no morality unless there is a deity. Put a little more fully, the argument in effect says that there can be no moral code unless it is laid down, policed, punished and rewarded by a deity… Or, alternatively put again: because god is so nice, we should be nice to each other.”
“The argument that there can be no morality unless policed by a deity is refuted by the existence of good atheists.” [Emphasis mine.]
Anthony Grayling The God Argument p.103f (kindle ed.)
I didn’t notice it until putting these two quotes side by side but notice how both Dennett and Grayling are keen to talk about the “simplest” versions of the arguments! The only problem is that these ‘simple’ versions are incorrect versions.  If I were reading this account of the moral argument for an A-level paper I would conclude the student was, at best, very confused about the argument, and at worst was making it up as they went along. This is, by far, one of the worst accounts of the moral argument I’ve ever read. How can it be that A-level students can understand this argument better than Anthony Grayling? I am yet to work that one out but I think this is a reason why one ought not be worried to hear that some professional philosophers are not impressed by arguments for the existence of God because there is evidence some of them don’t know them very well and/or they cannot describe them correctly.
4. In her book 36 Arguments for the Existence of God: A Work of Fiction (apt subtitle) philosopher Rebecca Goldstein makes a hash of a good number of the arguments. She proposes a cosmological argument like this:
1. Everything that exists must have a cause.
2. The universe must have a cause (from 1).
3. Nothing can be the cause of itself.
4. The universe cannot be the cause of itself (from 3).
5. Something outside the universe must have caused the universe (from 2 and 4).
6. God is the only thing outside the universe.
7. God caused the universe (from 5 and 6).
8. God exists.
Since I’ve already commented on that first premise when referencing Dennett I’ll let William Lane Craig respond to the rest:
“What’s funny is that Goldstein proceeds to point out two “flaws” in this conglomeration of statements masquerading as the cosmological argument. She doesn’t even pause to note that it’s not only logically invalid, but question-begging, since (8) follows from (6) alone, so that all the remaining premisses are just window-dressing. This straw man argument has never been defended by any philosopher in the history of thought.”
William Lane Craig 36 Arguments for the Existence of God: Goldstein on the Cosmological Argument 
Given that professional atheist philosophers appear to sometimes be out of their depth doing philosophy of religion in a technically correct fashion it ought not to be surprising that we find these arguments to be horribly wrong in works by atheist authors who have done little or no philosophy at all.
Examples like these suggest that Quentin Smith’s warning to atheist philosophers (that they are not keeping up with technical philosophy of religion well enough to be considered formally competent in the subject) about how well they are able to engage in the subject of philosophy of religion (written some 20 years ago now) has not been given the attention it deserves.
 See also this incredibly painful video interview where the Guardian’s religion writer Andrew Brown takes Dennett to the woodshed in just 5 minutes.
 See God, Freedom and Evil.
 I have more on how poor Grayling’s interaction is with the moral argument in my post Why I like the moral argument for God.