I feel as if I have been reading about the query process for years, and yet there is always more. A fellow member of my small writing group is also working on his query letter. His book is for a similar, though slightly older, age group, but it is a far different book. In any case, he has also been reading QueryShark and other sites.
The biggest mistakes that I have seen out there in query examples, aside from writing a book that nobody wants to publish because the market is saturated with vampires or the plot is way too similar to Harry Potter:
1) Not knowing what your book is really about. This sounds bizarre, but there do seem to be a number of people who write a whole lot about some characters without ever really grasping that there needs to be a real plot. If you don't have that plot, the query seems to ramble on about either the author or the kind of characters, but never communicate a sense of urgency or a sense of the stakes in the story for the MC. Often, the author wanted "to write a book" rather than write this book.
2) Inability to sell the story. This is far more common, and may happen even with a great book. Whether through paralysis or carelessness or something else, the author seems to say: Trust me, it's a great book, so I shouldn't have to describe it. Just read it. (As a software developer, this is akin to software companies that can't describe their products, but simply want you to discover it for yourself. I've never once bought software sold that way.)
3) Rushed and sloppy. An author may spend years writing a book, but then whips off a query letter and sends it, warts and all. Again, hard for me to believe, but it happens a lot. Usually, this is followed by zero offers for representation and the book being self-published filled with typos.
4) Arrogance. Some authors are convinced that the world should grovel at their feet because they wrote the masterpiece of all masterpieces, unique among books. Somehow, this comes through in a query letter.
5) The query doesn't follow the submission rules. While some agents may overlook some minor infractions, most seem to have too many queries to start with and are looking for queries to cull. If the agent has posted clear rules and the query doesn't follow them, it significantly raises the chance that the author will be a slightly better controlled version of #5.
There are obviously many other reasons why an agent will pass on a query, not all of which are "mistakes". They may have too many like that one, or it may not sound like a voice they like, or they may have had too much coffee and feel unable to read that afternoon. Your query may not be significantly flawed, but it is probably a good idea to assume it might be if nobody is asking for partials or fulls or showing any interest at all.